Commands help

brainvisa-cmake

aims-free

aims-til

anatomist-free

anatomist-gpl

axon

morphologist-private

baby

sulci-private

morphologist-ui

brainrat-private

bioprocessing

primatologist-gpl

constellation-private

cortical_surface-private

nuclear_imaging-private

longitudinal_pipelines

highres-cortex


brainvisa-cmake

bv_clean_build_treebv_copy_treebv_env
bv_env_hostbv_env_testbv_maker
bv_nobadlinkbv_packagingbv_projects_info
bv_releasebv_show_build_logsbv_sip4make
bv_system_infobv_unenvbv_unit_test
bv_whichbv_wine_regeditcgrep
cmgrepkdiff3_svnkompare_svn
meld_svnpygrepsvnclient

aims-free

Aims3DPointCloudAimsActivPixel2VolumeAimsAddNoise2Data
AimsApplyVectorFieldAimsAttributedViewerAimsAverage
AimsBuildDtiAimsBuildIndexAimsBundle2Vol
AimsBundleAnalysisAimsBundleSelectCenterAimsBvalue
AimsChamferDistanceMapAimsChannelExtractAimsCiftiSubMatrix.py
AimsClosingAimsClusterArgAimsCompareSPMtToPrimalSketch
AimsComposeTransformationAimsConnectCompAimsConvexHull
AimsCorrectionEpiAimsCreateTextureAimsCurvature2d
AimsCurvature3dAimsCylinderAimsDanielssonDist
AimsData2JpegAimsDicomAnonymize.pyAimsDilation
AimsDistordDtiAimsDtiBck2VolAimsElevationMap
AimsErosionAimsExtractLabelsFromTexture.pyAimsFiberOversampler
AimsFileConvertAimsFileInfoAimsFlip
AimsFoldArgAttAimsFoldsGraphOverSegmentation.pyAimsFoldsGraphThickness.py
AimsFovSplitAimsFrontDistanceMapAimsGTMDump
AimsGaussianSmoothingAimsGaussianSmoothing1dAimsGetTransformation.py
AimsGraphCompleteAimsGraphConvertAimsGraphExtractTransformation
AimsGraphMergeAimsGraphMeshAimsGraphTransferLabels
AimsGyriTextureCleaningIsolatedVertices.pyAimsHJEvolution2dAimsHJEvolution3d
AimsHippocampicReferentialAimsIcmSpaghettiAimsIcmSpaghettiN
AimsIcosaListAimsImageGLBlobStatsAimsImagePrimalSketch
AimsImageScaleSpaceAimsImageSmoothingAimsInflate
AimsInvertTransformationAimsKMeansAimsKMeansImageSegmentation
AimsLabelSelectorAimsLabels2TexAimsLightenAtlas
AimsLinearCombAimsMIRegisterAimsManualBiasCorrection
AimsMaskAimsMaskPhantomAimsMassCenter
AimsMeanCurvFlowAimsMedianSmoothingAimsMerge
AimsMerge2RgbAimsMergeLabelAimsMergeLabelsFromTexture.py
AimsMeshAimsMesh2AsciiAimsMesh2SSGraph
AimsMesh2SphereAimsMeshAreaAimsMeshAverage
AimsMeshBlobExtractAimsMeshBrainAimsMeshCC2Arg
AimsMeshCheckClosedAimsMeshConnectedComponentAimsMeshCurvature
AimsMeshCutAimsMeshDecimationAimsMeshDistance
AimsMeshGenerateAimsMeshGeodesicDepthAimsMeshLineMeasurement
AimsMeshParcellation2VolumeParcellationAimsMeshSmoothingAimsMeshTransform
AimsMeshWatershed.pyAimsMeshWhiteAimsMeshes2Graph
AimsMomentAimsMorphoMathAimsNormDiff
AimsNormWithRegionAimsOpeningAimsOverVolume
AimsPCAfilterAimsPCAlocAimsPCAloc2
AimsParamCorrectDtiAimsParameterize2DImageDomainAimsPowerComb
AimsRFdfAimsRTiffAimsRefineMesh
AimsRegisterBMEstimateAimsRegisterFFDApplyAimsRegisterFFDEstimate
AimsRegisterFFDFromCoordImagesAimsRemoveNaNAimsReplaceLevel
AimsResampleAimsRoiFeaturesAimsSNR
AimsSTAP.pyAimsSegmentsToMeshAimsSelectLabel
AimsSetMinfAimsSetTransformation.pyAimsSiemensEPI2Volume
AimsSimilarComponentAnalysisSegmentationAimsSlice2BucketAimsSmoothing
AimsSpaghettiModelAimsSparseMatrixToDense.pyAimsSphereDistribution
AimsSplitArrayAimsSplitRgbAimsSpmNormalizationConvert.py
AimsSubSamplingAimsSubTensorAimsSubVolume
AimsSulciVoronoi.pyAimsSulcusSPAMAimsSumFrame
AimsSumPETFrameAimsSumSparseMatrixAimsT1mapVFA.py
AimsT2BasedCorrectionEpiAimsTCatAimsTMSCone.py
AimsTMStargetAimsTalairachTransformAimsTensor2Bucket
AimsTensorExtractAimsTensorSNRAimsTex2Graph
AimsTex2VolAimsTexture2PrimalAimsTextureAverage
AimsTextureDerivativeAimsTextureDilationAimsTextureErosion
AimsTexturePrimalSketchAimsTextureRegularizationAimsTextureScaleSpace
AimsTextureSmoothingAimsTextureThresholdAimsTextureVoronoi
AimsThresholdAimsTopologicalClassificationAimsVFilter
AimsValidateFitAimsVectorFieldToMeshAimsVeinExtraction
AimsVoiStatAimsVolumeExtractAimsVolumeToTexture.py
AimsVoronoiAimsZCatEcatVolMIProj
EcatVolReversecartoFSLmatToTrm.pycartoGraphAddAttributeFromCsv.py
cartoGraphCat.pycartoGraphTransform.pycartoLinearComb.py
cartoSetMinf.py

aims-til

meshCleaner

anatomist-free

anatomistmkhierarchy-anatomist

anatomist-gpl

anaAtlasViewer.pyanaSulciSnapshot.pyanasimpleviewer.py
autocrop.pymosaic.py

axon

axon-runprocessbrainvisa

morphologist-private

VipAlternatedSequentialFilterVipAngleToDeplacementVipBiasCorrection
VipCSFSegVipClosingVipClusterArg
VipConnexFilterVipConvertVipCovarianceMatrix
VipCylinderVipDericheVipDilation
VipDistanceMapVipDoubleThresholdVipEpiCorrect
VipEpiDistParamVipEpiPhaseMapVipErosion
VipExtEdgeVipFileDumpVipFlip
VipFoetusHomotopicSnakeVipFoldArgVipFoldArgAtt
VipGaussianVipGeometryVipGetBrain
VipGetHeadVipGetSliceVipGreyStatFromClassif
VipGreyWhiteClassifVipHistoAnalysisVipHomotopic
VipHomotopicSnakeVipHysteVipLabelArg
VipLabelContourVipLabelMatchingVipLabelOverlap
VipLinCombVipLinearResampVipListLabel
VipMaskVipMatchingVipMerge
VipMinimizeInformationVipMomentVipOpenFold
VipOpeningVipPcaVipPreprocessing
VipSetPointValueVipSingleThresholdVipSkeleton
VipSplineResampVipSplitVipSplitBrain
VipSubVolumeVipSumFrameVipSwapEndian
VipT1BiasCorrectionVipTalairachCoordinatesVipTalairachTransform
VipTopoClassifMeaningVipTopoClassificationVipTransform
VipTriangleVipVFilterVipVoiStat
VipVoronoivip_test_well_composed_configurationsvip_test_well_composed_topology

baby

AimsTopHatBabyBrainHemiCutBabyBrainIntensityRange
BabyCGNCerebSegBabyCGNDetectionBabyDetectorNormalization
BabyHistoAnalysisBabyInterFissureMaskVipInfantHomotopicSnake

sulci-private

neurlearnneurmakenetneurpatimport
readFoldssiChangeModelssiCopyModelDescriptors.py
siCopyNamessiCsvMapGraph.pysiDiffModels.py
siDisplayGraph.pysiDisplayGrid.pysiDivNameList
siDomTrainsiEnergysiError
siErrorLightWrapper.pysiErrorStatssiFlip
siFoldGraph2vrml.pysiFunctionalGraphssiGenerateLearningTasks.py
siGraph2LabelsiGraphSwithNameLabel.pysiGraphToCsv.py
siLearnsiLearn.pysiLyxErrors
siMakeColoredHierarchysiMakeModelsiMakeParcellationHierarchy
siMergeModelssiMeshSulciOperturesiMeshSulciProjection
siMkModelEdgessiModelsErrorRateInfo.pysiMonitor.py
siMorphosiMultilabelComparesiPIDcommand
siParcellationsiPotentialSummary.pysiPutTextureInModel
siRelaxsiRelax.pysiRevert
siSulcalParcellationsiSynthRelaxResult.pysiTestModels
siTestModels.pysiTriangModelsiTryGauss
sigraph-configsulciCurvature.pysulciDistanceToLesion.py
sulciDistanceToNeighbours.pysulciLabelConsistencyCheck.pysulciReplaceDescriptors.py
sulciSulcuswisePotentials.py

morphologist-ui

morphologist

brainrat-private

AimsAdaptiveSelVoxelAimsAxialProjectionAimsBorderGenerate
AimsBorderInfoAimsCenterSlicesAimsFovAdapt
AimsGL2ActivityAimsIndividStackSlicesAimsInterSliceNormalize
AimsManualRegistrationAimsMidPlaneAlignAimsReadDpy
bioModelClassifybioModelGeneratebioReadDpy

bioprocessing

AimsAffineRegisterAimsAmyloidDensityAimsAmyloidDetection
AimsAmyloidFilteringAimsAmyloidLoadAvgDistNeighAimsAmyloidLoadInvSurfVor
AimsAmyloidMRIDetectionAimsAreaNbConnectCompRatioAimsBinaryBorder
AimsBinaryBoundingBoxAimsBorderCropAimsBorderLineProj
AimsBoundingBoxCalculationAimsBoundingBoxExtractionAimsChannelProcess
AimsComponentFeaturesAimsComponentFeaturesMapGenerateAimsComponentFeaturesProcess
AimsComponentFeaturesVisualizeAimsCorrectImagesAimsCreateFieldsFromMotion
AimsEntropicThresholdingAimsEqualizerAimsFovCentering
AimsGenerateVolumeAimsGridCalibrateAimsGridGenerate
AimsHeightFilteringAimsIndexClusterAimsIndividSlices
AimsInterlaceVolumesAimsLabelReorderAimsMIBucketRegister
AimsMaskContourAimsMergeFFDLabelsAimsMeshMatching
AimsMidPlaneMaskAimsMosaicAimsMultiRecal
AimsOverlapInfoAimsPointsExtremeAimsRebuildComp
AimsResampleFromFieldsDataAimsRgbToHsvAimsRoiOverlap
AimsSamplingInfoAimsSeededWatershedAimsSegment2Modes
AimsSeparateCompAimsStereologySamplingAimsStereotaxy
AimsWatershedbioClusterStatisticsbioExtractAmyloidLoad
bioExtractDicebioFindCellSeedsbioMacGetSingleBrain
bioVoxelFeaturesbioVoxelWiseStatistics

primatologist-gpl

AimsRegisterQNEstimateAimsSegmentationEMAimsSelectGradPoints
bioKMeans

constellation-private

AimsSparseMatrixSmoothingconstelBundlesFilteringconstelConnectionDensityTexture
constelConnectivityMatrixconstelFibersLengthsconstelMeanConnectivityProfileFromMatrix
constelSelectBundlesFromNamesconstelSelectFibersFromMesh

cortical_surface-private

AimsCheck2DCoordinatesAimsConformalMappingAimsConstraintCleaner
AimsCoordinateGridMeshAimsCoordinatesTextureToMeshAimsCoordinatesToIndex
AimsCoordinatesToTextureAimsCorticalReferentialAimsCorticalThickness
AimsExactDepthAreaAimsExtractGyrusAimsFlattenCortex
AimsFunctionProjectionAimsGeodesicPathAimsGroupGyri
AimsGyriRegularizationAimsGyriStuffAimsInterpolateVolumeToSurface
AimsMeshCoordinatesToDecimatedAimsMeshIsoLineAimsMeshMedianSurface
AimsMeshToAtlasAimsMeshToMeshPointAimsParameterizeGyri
AimsParameterizeSulcusAimsPlotCoordinatesOnMeshAimsPlotOnSPhericalAtlas
AimsSulcalLinesAimsSulcusCorticalSnakeAimsSulcusNormalizeDepthProfile
AimsTextureCompareAimsTextureToAtlasPlotFociForValidation
surfStructuralAnalysissurfTexActivationSimulation

nuclear_imaging-private

AimsPETInjectedDoseNormalize

longitudinal_pipelines

BsiBSIBsiDiffMaskBsiNormIntensity

highres-cortex

ylAdvectEuclideanylAdvectPathylAdvectTubes
ylAdvectValuesylIsoCurvatureylLabelEachVoxel
ylLaplacianylMakeTraversePseudoAreaMapylMergeCortexColumnRegions
ylPropagateAlongFieldylUpwindDistance

bv_clean_build_tree

Usage: bv_clean_build_tree [options] [dirnames]

Clean build directory / directoriesIf no dir is specified, the current
directory is assumed.Dead links and obsolete python modules (.pyc and .pyo
files without a valid .py file next to them) are removed.

Options:
  -h, --help            show this help message and exit
  -a ACCESSTIME, --accesstime=ACCESSTIME
                        delete files that have older access time than the one
                        specified.
  -b, --bin             also check if all entries in bin/ are still present in
                        Makefile, or obsolete, and erase them if not. Needs to
                        have configured and up-to-date Makefiles
  -d, --dir             remove empty directories. Do not use this option
                        during compilation, since it may remove some useful,
                        temporarily empty, directories...
  -l, --list            only list files and directories that will be deleted,
                        do not delete those.

bv_copy_tree

Usage: bin/bv_copy_tree [options] source1 [source2] [...] destCopy directories trees, like "cp -a" or "rsync -a --copy-unsafe-links", but try to preserve internal symlinks, and keep a unique copy of actual files for external symlinks.


Options:
  -h, --help            show this help message and exit
  -b BASE, --base=BASE  base directory to consider external symlinks. Default
                        is input directories. Several -b options may be
                        passed.
  -s, --simulation      do not perform actual copies, don't write anything,
                        just tell what will be done (use with -v option)
  -v, --verbose         say what is done
  -e EXCLUDE, --exclude=EXCLUDE
                        exclude some (source) directories from copies. Several
                        -e options may be passed.

bv_env

bv_env [command [command_arg [...]]]

run a command in brainvisa-cmake paths environment.

Without arguments, print the runtime environment to be used on the standard output
With arguments, set the runtime environment, and run the command passed in arguments in this environment.

bv_env_host

bv_env [command [command_arg [...]]]

run a command in brainvisa-cmake paths environment.

Without arguments, print the runtime environment to be used on the standard output
With arguments, set the runtime environment, and run the command passed in arguments in this environment.

bv_env_test

./bin/bv_env -h
bv_env [command [command_arg [...]]]

run a command in brainvisa-cmake paths environment.

Without arguments, print the runtime environment to be used on the standard output
With arguments, set the runtime environment, and run the command passed in arguments in this environment.

bv_maker

Usage: bv_maker [options] [ command [command options] ]...

This program is for the management of source retrieval, configuration and compilation of BrainVISA projects.

In order to work, the commands svn and svnadmin must be installed on your system. On some Linux systems they are in two separate packages (e.g. subversion and subversion-tools).

Commands:

* info: Just output info about configured components.
* sources: Create or updated selected sources directories from Subversion
  repository.
* configure: Create and configure selected build directories with CMake.
* build: compile all selected build directories.
* doc: Generate documentation (sphinx, doxygen, docbook, epydoc).
* testref: Execute tests in a special mode to generate machine-specific
  reference files (this is needed by some tests).
* test: Execute tests using ctest.
* pack: Generate binary packages.
* install_pack: Install binary packages.
* testref_pack: Create the machine-specific reference files for tests in
  installed binary package.
* test_pack: Run tests in installed binary packages.
* publish_pack: Publish binary packages.

To get help for a specific command, use -h option of the command. Example: "bv_maker build -h".

To get help on how to configure and write a bv_maker configuration file, see:

http://brainvisa.info/brainvisa-cmake/compile_existing.html

config file syntax:

http://brainvisa.info/brainvisa-cmake/configuration.html

and more generally:

http://brainvisa.info/brainvisa-cmake/


Options:
  -h, --help            show this help message and exit
  -d DIR, --directory=DIR
                        Restrict actions to a selected directory. May be used
                        several times to process several directories.
  -c CONFIG, --config=CONFIG
                        specify configuration file. Default
                        ="/home/dr144257/.brainvisa/bv_maker.cfg"
  -s DIR, --sources=DIR
                        directory containing sources
  -b DIR, --build=DIR   build directory
  --username=USERNAME   specify user login to use with the svn server
  -e, --email           Use email notification (if configured in the general
                        section of the configuration file)
  --disable-jenkins     disable Jenkins server logging
  -v, --verbose         show as much information as possible
  --version             show bv_maker (brainvisa-cmake) version number

bv_nobadlink

bin/bv_nobadlink [directory1 [directory2 [...]]]:
recursively remove dead links in the given directories (default: current directory)

bv_packaging

bv_packaging [options] <package_type> [ <selection_rule> ... ]

  This program is for the creation of packages and dependency graph for build directories.

  Package types:
    list: Only list selected packages
    dot: Create a Graphviz dependency graph for selected packages
    dir: Create a single directory containing all selected packages
    pack: Like "dir" but compress the result in a *.tar.bz2 archive
    deb: Create a debian package for each selected packages

  Selection rule:
    +<selection_pattern>: Adds all packages corresponding to the selection pattern
    -<selection_pattern>: Remove all packages corresponding to the selection pattern
    +dependencies: Special rule to add the dependencies of the currently selected packages

  Selection pattern:
    <property>=<pattern>[,<property>=<pattern>...]: match all packages where every selected property match the corresponding pattern
    <pattern>: equivalent to name=<pattern>

  Packages properties:
    name: Name of the package
    type: Type of the package
    version: Package version
    project: Name of the project containing the package.
    maintainer: Name of the maintainer of the package

  Package types:
    run: Runtime package
    dev: Development package
    doc: Documentation package
    usrdoc: User documentation package
    devdoc: Developper documentation package
    test: Test files package
    thirdparty: Package corresponding to a thirdparty project not compiled in the build directory

  Default selection rule:
    +type=run: select all

  Examples:
    Create a dependency graph for runtime packages
      bv_packaging -o /tmp/dependency-run.dot dot

    Create a dependency graph for development packages
      bv_packaging -o /tmp/dependency-dev.dot dot +type=dev

    Create debian packages for all runtime packages in soma project
      bv_packaging deb +project=soma,type=run

    Create debian packages for all runtime packages except brainvisa-system:
      bv_packaging deb +type=run -name=brainvisa-system

    List all packages whose name start with "a" excludind development packages
    without their dependent packages:
      bv_packaging --no-deps list '+a*'

    Create debian packages for all packages in soma project with all their dependencies except python
      bv_packaging deb +project=soma +dependencies -python


Options:
  -h, --help            Show this help message and exit
  -v, --verbose         Show verbose information
  -o OUTPUT, --output=OUTPUT
                        File (without extension) or directory where output will be stored.
  -m MAKE_OPTIONS, --make-options=MAKE_OPTIONS
                        Options to pass to make during packages creation.
  --bv_env              Replace commands located in bin directory by a script that calls
                        the command through bv_env.
  --wrappers            same as --bv_env, but do not copy the executable bv_env
                        and sibling scripts in the package directory: just do
                        the wrapping scripts
  --packname            Obsolete. Does nothing. Now the name of the package is always
                        included in the compressed archive.
  --compressed-packdir  Name of the directory in compressed archive.
                        Available only with pack command. By default, the name of the directory in the archive is the name of the pack.
  --tmp DIRECTORY       Location of temporary directory (default is '/tmp').
  --cmake CMAKE_EXE     Location of cmake executable (default = 'cmake').
  --installer           bv_packaging is used for the bv_build_installer tool:
                        changes only the way the brainvisa-release component
                        is installed.
  --platform-target PLATFORM
                        platform target for cross compilation.


bv_projects_info

Usage: bv_projects_info <projects> [options] 

Display information about brainvisa projects.



Options:
  -h, --help    show this help message and exit
  --no-trunk    Do not display trunk.
  --no-release  Do not display releases.
  --no-bug_fix  Do not display bug_fixes.

bv_release

Usage: bv_release <branch_type> <projects> [options]

Create a bug fix or a release branch of the given projects with the given
version number. If the version is not indicated, a new version number is created
from the last existing version number. The type of branch can be 'bug_fix' to
move branches/bug_fix to branches/X.Y and copy trunk to branches/bug_fix branch
or 'release' to move tags/latest_release to tags/X.Y.Z and copy branches/bug_fix
to tags/latest_release. The project_info.cmake files in each component will be
updated with the new version number. The trunk version is merged in order to
validate the differences in project_info.cmake files.

Equivalent svn commands:
svn copy --parents project/trunk project/branches/version -m "Creating a version bug fix branch of the project."
svn copy --parents project/trunk project/tags/version -m "Creating a version release branch of the project."


Options:
  -h, --help            show this help message and exit
  -v VERSION, --version=VERSION
                        Version number of the branch: X.Y for a bug fix
                        branch, X.Y.Z for a release branch.
  -s, --simulation      Do not execute the svn commands, just show the
                        commands.
  --no-branch           Do not create branches.
  --no-update           Do not update the project info file.
  --no-auto-merge       Disable automatic merge of project info file.
  --force               Force processing in cases of inconsitencies.
  -q                    Quietly run without displaying information.

bv_show_build_logs

Usage: Display BrainVisa build logs in a GUI

Options:
  -h, --help            show this help message and exit
  -i LOGFILE, --input=LOGFILE
                        input log file(s) [default:
                        ['/neurospin/brainvisa/build/builds.log']]
  -s SSH_HOST, --ssh=SSH_HOST
                        remote host for ssh access. default: is208611. Only
                        used if the log file cannot be found on the local
                        filesystem.
  -u USER, --user=USER  user for ssh access. default: not specified, use
                        current one

bv_sip4make

Usage:
    sip [-h] [-V] [-a file] [-b file] [-B tag] [-c dir] [-d file] [-e] [-g] [-I dir] [-j #] [-k] [-m file] [-o] [-p module] [-P] [-r] [-s suffix] [-t tag] [-T] [-w] [-x feature] [-X id:file] [-z file] [@file] [file]
where:
    -h          display this help message
    -V          display the sip version number
    -a file     the name of the QScintilla API file [default not generated]
    -b file     the name of the build file [default none generated]
    -B tag      add tag to the list of timeline backstops
    -c dir      the name of the code directory [default not generated]
    -d file     the name of the documentation file (deprecated) [default not generated]
    -e          enable support for exceptions [default disabled]
    -g          always release and reacquire the GIL [default only when specified]
    -I dir      look in this directory when including files
    -j #        split the generated code into # files [default 1 per class]
    -k          support keyword arguments in functions and methods
    -m file     the name of the XML export file [default not generated]
    -o          enable the automatic generation of docstrings [default disabled]
    -p module   the name of the consolidated module that this is a component of
    -P          enable the protected/public hack
    -r          generate code with tracing enabled [default disabled]
    -s suffix   the suffix to use for C or C++ source files [default ".c" or ".cpp"]
    -t tag      the version/platform to generate code for
    -w          enable warning messages
    -x feature  this feature is disabled
    -X id:file  create the extracts for an id in a file
    -z file     the name of a file containing more command line flags
    @file       the name of a file containing more command line flags
    file        the name of the specification file [default stdin]

bv_system_info

 Get system identification information 
       -p or --platform option gives a general information about the platform (linux, windows, irix, macos, solaris)
       -s or --shortname option gives a system shortname without architecture
       -h or --help option display this help

bv_unenv

bv_unenv [command [command_arg [...]]]
Reset original environment (that was active before using bv_env)
Without arguments, print the runtime environment to be used on the standard output
With arguments, set the runtime environment, and run the command passed in arguments in this environment.

bv_unit_test

Usage: bv_unit_test case1 [case2] [...]

Run predefined unit tests cases.

Options:
  -h, --help  show this help message and exit

bv_which

Usage: bv_which [options] name [name...]

Look for files in environment variables containing paths. Both the found file
name and the real file name (without any symbolic link in its path) are
displayed. It is possible to use shell-like patterns for name to find.

Options:
  --version             show program's version number and exit
  -h, --help            show this help message and exit
  -v VARIABLES, --variable=VARIABLES
                        Adds a path environment variable. If none is given,
                        PATH, LD_LIBRARY_PATH and PYTHONPATH are used.

bv_wine_regedit

usage: bv_wine_regedit [-h] [-f REGISTRY_FILE] [-p PREFIX]
                       [-r REGISTRY_ACTION] [--value-path VALUE_PATH]
                       [--value VALUE]

Update registry with missing pathes.

optional arguments:
  -h, --help            show this help message and exit
  -f REGISTRY_FILE, --registry-file REGISTRY_FILE
                        Wine registry file to update [default: None].
  -p PREFIX, --prefix PREFIX
                        Install prefix to use [default: None].
  -r REGISTRY_ACTION, --registry-action REGISTRY_ACTION
                        action to do in registry [default: set].
  --value-path VALUE_PATH
                        path of the value to set in registry [default: None].
  --value VALUE         the value to set in registry [default: ].

cgrep

Utilisation : grep [OPTION]... MOTIF [FICHIER]...
Exécutez « grep --help » pour obtenir des renseignements complémentaires.

cmgrep

Utilisation : grep [OPTION]... MOTIF [FICHIER]...
Exécutez « grep --help » pour obtenir des renseignements complémentaires.

kdiff3_svn

Usage : kdiff3 [options-Qt] [options-KDE] [options] [File1] [File2] [File3] 

Outil de comparaison et de fusion de fichiers et de dossiers

Options génériques :
  --help                    Afficher l'aide sur les options
  --help-qt                 Afficher les options spécifiques à Qt
  --help-kde                Afficher les options spécifiques à KDE
  --help-all                Afficher toutes les options
  --author                  Afficher les informations sur l'auteur
  -v, --version             Afficher les informations sur la version
  --license                 Afficher les informations sur la licence
  --                        Fin des options

Options :
  -m, --merge               Fusionner les entrées.
  -b, --base file           Fichier de base explicite. Pour la compatibilité avec certains outils.
  -o, --output file         Fichier de sortie. Implique -m. Par ex. : -o nouveaufichier.txt
  --out file                Fichier de sortie, encore. (Pour la compatibilité avec certains outils)
  --auto                    Pas d'interface graphique si tous les conflits se résolvent automatiquement. (Nécessite un fichier -o)
  --qall                    Don't solve conflicts automatically.
  --L1 alias1               Remplacement de nom visible pour le fichier d'entrée 1 (base).
  --L2 alias2               Remplacement de nom visible pour le fichier d'entrée 2.
  --L3 alias3               Remplacement de nom visible pour le fichier d'entrée 3.
  -L, --fname alias         Remplacement de nom visible secondaire. À fournir une seule fois pour chaque entrée.
  --cs string               Annuler un paramètre de configuration. À utiliser une seule fois pour chaque paramètre. Par ex. : --cs « AutoAdvance=1 »
  --confighelp              Afficher la liste des paramètres de configuration et les valeurs actuelles.
  --config file             Utiliser un fichier de configuration différent.

Arguments :
  File1                     fichier 1 à ouvrir (base, si non spécifié, via --base)
  File2                     fichier 2 à ouvrir
  File3                     fichier 3 à ouvrir
  -u, --ignore              Ignoré. (Défini par l'utilisateur)
  --query                   Ignoré. (Défini par l'utilisateur)
  --html                    Ignoré. (Défini par l'utilisateur)
  --abort                   Ignoré. (Défini par l'utilisateur)

kompare_svn

Utilisation : kompare [options]
A program to view the differences between files and optionally generate a diff

Options :
  -v, --version              Afficher les informations de version.
  -h, --help                 Afficher cette aide.
  --author                   Afficher les informations sur l'auteur.
  --license                  Afficher les informations sur la licence.
  --desktopfile <file name>  The base file name of the desktop entry for this
                             application.
  -c                         This will compare URL1 with URL2
  -o                         This will open URL1 and expect it to be diff
                             output. URL1 can also be a '-' and then it will
                             read from standard input. Can be used for instance
                             for cvs diff | kompare -o -. Kompare will do a
                             check to see if it can find the original file(s)
                             and then blend the original file(s) into the
                             diffoutput and show that in the viewer. -n disables
                             the check.
  -b                         This will blend URL2 into URL1, URL2 is expected
                             to be diff output and URL1 the file or folder that
                             the diffoutput needs to be blended into. 
  -n                         Disables the check for automatically finding the
                             original file(s) when using '-' as URL with the -o
                             option.
  --e <encoding>             Use this to specify the encoding when calling it
                             from the command line. It will default to the local
                             encoding if not specified.

meld_svn


(meld:31915): Gtk-WARNING **: Invalid input string

(meld:31915): Gtk-WARNING **: Invalid input string

(meld:31915): Gtk-WARNING **: Invalid input string

(meld:31915): Gtk-WARNING **: Invalid input string

(meld:31915): Gtk-WARNING **: Invalid input string

(meld:31915): Gtk-WARNING **: Invalid input string

(meld:31915): Gtk-WARNING **: Invalid input string

(meld:31915): Gtk-WARNING **: Invalid input string

(meld:31915): Gtk-WARNING **: Invalid input string

(meld:31915): Gtk-WARNING **: Invalid input string

(meld:31915): Gtk-WARNING **: Invalid input string

(meld:31915): Gtk-WARNING **: Invalid input string

(meld:31915): Gtk-WARNING **: Invalid input string

(meld:31915): Gtk-WARNING **: Invalid input string
Usage: 
  meld                                 Démarrer avec une fenêtre vide
  meld <fichier|folder>                Démarrer une comparaison de gestion de versions
  meld <fichier> <fichier> [<fichier>] Démarrer une comparaison de 2 ou 3 fichiers
  meld <folder> <folder> [<folder>]    Start a 2- or 3-way folder comparison

Meld est un outil de comparaison de fichiers et de répertoires.

Options:
  --version             show program's version number and exit
  -h, --help            show this help message and exit
  -L LABEL, --label=LABEL
                        Définit l'étiquette à utiliser au lieu du nom de
                        fichier
  -n, --newtab          Open a new tab in an already running instance
  -a, --auto-compare    Compare automatiquement tous les fichiers différents
                        au démarrage
  -u, --unified         Ignorée pour compatibilité
  -o OUTFILE, --output=OUTFILE
                        Définit le fichier cible pour l'enregistrement d'un
                        résultat de fusion
  --auto-merge          Automatically merge files
  --comparison-file=COMPARISON_FILE
                        Load a saved comparison from a Meld comparison file
  --diff                Create a diff tab for the supplied files or folders


pygrep

Utilisation : grep [OPTION]... MOTIF [FICHIER]...
Exécutez « grep --help » pour obtenir des renseignements complémentaires.

svnclient

Usage: svnclient <sub-command> [options] [parameters]

This command enables to create a custom client for a subversion repository. You can choose the subdirectories of the repository that you want to see in your client.
First, create the client directory using svnclient create DIRECTORY.
Then, choose the content of your client using svnclient edit [DIRECTORY]. This opens an editor with the current list of directories of the client. The format of the file is: <client path> <repository path>. Comment lines begin with #.
Update the client using svn update [DIRECTORY].

This command creates a local repository with an externals property that defines links to the actual repository. If there are several directory levels in the client definition, only the last directory is a work copy where svn commands are directory usable. But if you want to execute svn commands in all the client or in an intermediate directory of the client, you can use some svnclient options like: svnclient commit|ci [DIRECTORY] [-m MESSAGE].
       
       svnclient create DIRECTORY
       svnclient edit [DIRECTORY]
       svnclient show [DIRECTORY]
       svnclient commit|ci [DIRECTORY] -m MESSAGE
       svnclient status|st [DIRECTORY]
       svnclient update|up [DIRECTORY]
      
DIRECTORY can be a subdirectory of the client directory.

In order to work, the commands svn and svnadmin must be installed on your system. On some Linux systems they are in two separate packages (e.g. subversion and subversion-tools).

Options:
  -h, --help            show this help message and exit
  -m MESSAGE, --message=MESSAGE
                        specify log message for commit
  --username=USERNAME   specify user login to use with the svn server

Aims3DPointCloud


    Aims3DPointCloud
    ----------------

Generates cloud of 3D points

Options :

-i | --input <string>
    input coordinates file 

-o | --output <filename: Mesh of VOID>
    output mesh

-r | --radius <FLOAT>
    sphere radius

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsActivPixel2Volume


    AimsActivPixel2Volume
    ---------------------

Convert an Activ pixel list file into a volume

Options :

-i <file name (read only): volume of S16>
    origin file

-p <string>
    activ pixels list file

[ -o <filename: volume of S16> ]
    output image [default=input]

[ -l <S16> ]
    filling value [default=255]

[ -x <FLOAT> ]
    value of translation along x axis [default=0.0]

[ -y <FLOAT> ]
    value of translation along y axis [default=0.0]

[ -z <FLOAT> ]
    value of translation along z axis [default=0.0]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsAddNoise2Data


    AimsAddNoise2Data
    -----------------

Add gaussian or uniform noise to data

Options :

-i | --input <string>
    input data file

-o | --output <string>
    output data file

[ -m | --mean <FLOAT> ]
    mean of the Gaussian distribution [default=0.0]

[ -s | --sigma <FLOAT> ]
    standard deviation of the Gaussian distribution

[ -u | --uniform <boolean> ]
    take a uniform distribution rather than gaussian

[ -I | --Inferior <FLOAT> ]
    lowest value of uniform distribution

[ -S | --Superior <FLOAT> ]
    highest value of uniform distribution

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsApplyVectorField


    AimsApplyVectorField
    --------------------

Apply a vector field to a simple mesh or to all meshes of a fold graph

Options :

-i | -input <string>
    input mesh/graph data

[ -o | -output <string> ]
    output mesh/graph (default: trans_input)

-t | -target <string>
    target volume header

-v | -vectorfield <string>
    vector field prefix (will add .x, .y and .z)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsAttributedViewer


    AimsAttributedViewer
    --------------------

Displays attributed objects (.minf...) in a list view. AimsAttributedViewer can
also show any file header supported by AIMS IO system, just like AimsFileInfo

Options :

[ -i <string> ]
    file to display

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsAverage


    AimsAverage
    -----------

Averages several volume files or several images / slices of a file

Options :

-o | --output <string>
    output data

[ -t | --type <string> ]
    output data type (S16, U8, FLOAT, ...)

[ -d | --dir <string> ]
    if specified, perform averaging inside each file along this direction (x, y,
    z or t)

[ -n | --num <string> ]
    if a direction is specified, gives the volume or slice numbers to process.
    ex: 2-20,24,26 (no space between numbers)

-i | --input <vector of string>
    input volumes

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsBuildDti


    AimsBuildDti
    ------------

Estimation of the Tensor Diffusion from a diffusion MR image

Options :

-i <file name (read only): volume of S16>
    Diffusion image

[ -b <FLOAT> ]
    bvalue used during acquisition (default = read from image)

[ -dti <filename: bucket of DTITENSOR> ]
    DTI tensor output file name (default = not saved)

[ -m <string> ]
    Mask of brain or white matter

[ -tr <filename: volume of FLOAT> ]
    trace output file (default = not saved)

[ -vr <filename: volume of FLOAT> ]
    volume ratio output file (default = not saved)

[ -fa <filename: volume of FLOAT> ]
    fractional anisotropy output file (default = not saved)

[ -dir <filename: volume of POINT3DF> ]
    directions output file (default = not saved)

[ -rgb <filename: volume of RGB> ]
    RGB directions output file (default = not saved)

[ -em <filename: volume of U8> ]
    Binary mask of bad voxels (default = not saved)

[ -g <FLOAT> ]
    gamma diffusion coefficient for protons (default=42,57e6 . 2 Pi)

[ -r <boolean> ]
    when a point is NOT_POSITIVE_MATRIX, replace by an isotropic tensor which
    mean diffusivity is estimated on the N26 neighborhood of the point rather
    than the mean diffusivity equal to trace / 3.0

[ --correct <FLOAT> ]
    correct sites with negative eigen value

[ -verbose <boolean> ]
    show as much information as possible

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsBuildIndex


    AimsBuildIndex
    --------------

Extract trace,frationnal and relative anisotropy, volume ratio, directions,
coherence index, lattice index, linear, planar and spherical measures from
dtitensor bucket

Options :

-i | --input <file name (read only): bucket of DTITENSOR>
    source dtitensor bucket

[ -o | --output <string> ]
    destination base file name

-x <S32>
    dimensions of output images

-y <S32>
    dimensions of output images

-z <S32>
    dimensions of output images

[ --trace <boolean> ]
    calculate trace <fileout_trace.ima>

[ --l1 <boolean> ]
    calculate largest eigenvalue <fileout_lambda1.ima>

[ --l2 <boolean> ]
    calculate second eigenvalue <fileout_lambda2.ima>

[ --l3 <boolean> ]
    calculate third eigenvalue <fileout_lambda3.ima>

[ --fa <boolean> ]
    calculate fractionnal anisotropy <fileout_fa.ima>

[ --vr <boolean> ]
    calculate volume ratio <fileout_vr.ima>

[ --dir <boolean> ]
    calculate the main direction <fileout_dir.ima>

[ --ra <boolean> ]
    calculate relative anisotropy <fileout_ra.ima>

[ --ci <boolean> ]
    calculate coherence index  <fileout_ci.ima>. NB: This index is computed in
    2D which seems meaningless

[ --li <boolean> ]
    calculate lattice index <fileout_li.ima>

[ --m <boolean> ]
    calculate linear, planar and spherical measures <fileout_linear.ima>,
    <fileout_planar.ima>, <fileout_spherical.ima>

--all <boolean>
    calculate all maps

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsBundle2Vol


    AimsBundle2Vol
    --------------

Make an image of the bundles density
All bundles in the same volume

Options :

-i <string>
    bundles input

-r <file name (read only): carto_volume of S16>
    input image template

-o <filename: carto_volume of S32>
    bundles ima output

[ -m <S32> ]
    mode=1->mask,
    mode=2->count(NN)
    mode=3->count(LinearInterpol)
    default=2
    mode 3 doesn't work!!!

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsBundleAnalysis


    AimsBundleAnalysis
    ------------------

This command can be used for several purposes :

* Get quantitative information about bundles. This information is written in a
text file containing a table (one column per information, one row per bundle).
See -o and --imageStatistics options.

* Transform a bundle in another bundle according to several filters. See -t,
--split and -o options.

* Convert a bundles file to an Anatomist graph. See -g option.

Options :

-i <string>
    Bundles input file

[ -t <string> ]
    Transformation matrix to apply to input file (default: no transformation).
    The transformation is applyed before any other processing.

[ --selectionROI <string> ]
    ROI graph that will be used to select fibers and put them in bundles
    according to the rule file from --selectionRules parameter.

[ --selectionROITransformation <string> ]
    Transformation matrix to apply to selection ROI graph (option
    --selectionROI). Default: no transformation.

[ --selectionRules <string> ]
    Name of file containing selection rules. This option must be used if and
    only if --selectionROI is used.

[ --selectionOverlap <FLOAT> ]
    Percentage of point of a fascicle that have to be in a ROI to consider that
    the ROI is touched by the fascicle. 0 (the default) means that only one
    point in the ROI is engough, and 100 mean that all the fascicle points must
    be inside a ROI. This option is used only with --selectionROI.

[ --split <string> ]
    ROI graph that will be used to split the input bundle curves according to
    the ROI boundaries. This option transform the input bundle in another
    splitted bundle. The splitted bundle is used for processing that generate
    output.

[ --splitTransformation <string> ]
    Transformation matrix to apply to split ROI graph (option --split).
    Default: no transformation.

[ --splitKeepBundle <boolean> ]
    Keeps each fascicle original bundle name in output bundle (default =
    false). 

[ --minimumLength <DOUBLE> ]
    If greater than 0, all curves whose length is below minimumLength are
    ignored. This curve filtering is applied after all bundle transformation
    (-t and --split options) and before any other processing. Default value is
    0 (i.e. no filtering).

[ --imageStatistics <vector of string> ]
    Compute statistics from a 3D image. All bundle points are projected in the
    image to get a voxel value (with trilinear interpolation). For each bundle,
    the mean, standard deviation, minimum and maximum of voxel values are
    stored in the result file. Each argument of this parameter must have the
    syntax <label>:<filename> where <label> is a label and <filename> is a 3D
    image file name. For each argument, three columns are added in the result
    file: <label>_mean, <label>_stddev, <label>_min and <label>_max.

[ --slices <U64> ]
    number of slices in which each bundle is cut

[ --slicesMesh <filename: Segments of VOID> ]
    Generate a mesh allowing to check the shape of the slices.

[ -o <string> ]
    Generate a text file containing quantitative information about the bundles.
    The file contains the following fields (in addition to the fields coming
    from --imageStatistics option):
    curves_count: the number of curves in a bundle
    points_count: the total number of curves points in a bundle
    length_mean: the mean curves length in a bundle.
    length_stddev: the standard deviation of curves length in a bundle.
    length_min: the minimum of curves length in a bundle.
    length_max: the maximum of curves length in a bundle.

[ -g <string> ]
    Create and save an ROI graph containing one node per bundle and meshes to
    visualize curves in Anatomist.

[ -b <string> ]
    Save the bundles resulting from all requeted transformation applied to
    input bundles (options -t and --split)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsBundleSelectCenter


    AimsBundleSelectCenter
    ----------------------

Selects the centroid fiber from distance matrix

Options :

-i <string>
    bundle input file

-o <string>
    bundle output file

[ -dist_type <S32> ]
    fiber distance, 
    0: mean of two mean closest point distance (default), 
    1: max of two mean closest point distance, 
    2: maximum distance between corresponding points, 
    3: maximum distance between corresponding points normalized by fibers
    length

[ -normFactor <S32> ]
    Length normalization factor (only for dist_type=3) (default: 5.0)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsBvalue


    AimsBvalue
    ----------

B matrices for diffusion tensor sequence parameters

Options :

-i | --input <string>
    source EPI sequence

-o | --output <string>
    output volume name

[ -e | --eps <FLOAT> ]
    integration relative error [1e-5]

[ -j | --jmax <S32> ]
    maximum iteration number during integration [22]

[ -k <S32> ]
    interpolation order for Romberg integration [10]

[ -a | --agrad <S32> ]
    save gradients gx,gy,gz and their integrals

[ -g | --gamma <FLOAT> ]
    gamma diffusion coefficient for protons [default=42,57e6 . 2 Pi]

[ -b | --bipolar <S32> ]
    bipolar gradients [default=no]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsChamferDistanceMap


    AimsChamferDistanceMap
    ----------------------

Chamfer distance map on a volume

Options :

-i | --input <file name (read only): volume of S16>
    source volume

-o | --output <filename: volume of FLOAT>
    destination volume

[ -x | --xmask <S32> ]
    X size of the distance mask [default=3]

[ -y | --ymask <S32> ]
    Y size of the distance mask [default=3]

[ -z | --zmask <S32> ]
    Z size of the distance mask [default=3]

[ -f | --factor <FLOAT> ]
    chamfer multiplication factor [default=50]

[ -s | --side <string> ]
    OUTSIDE, INSIDE, SIGNED [default=SIGNED]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsChannelExtract


    AimsChannelExtract
    ------------------

Extract channel(s) of multichannel files

Options :

-i <string>
    input data

-o <vector of string>
    output file(s)

[ -c <vector of S32> ]
    channel(s) to extract

[ -t <string> ]
    output data type [default: U8]

[ -a <boolean> ]
    append channel suffix [default: true]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose | -v [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsCiftiSubMatrix.py

usage: AimsCiftiSubMatrix.py [-h] [-i CIFTI] [--gyri GYRI] [--gyrus GYRUS]
                             [-o OUTPUT]

Extract a submatrix from a CIFTI file for one gyrus or several gyri. The
extracted submatrix is in the shape currently expected by the Constellation
toolbox and Anatomist viewers.

optional arguments:
  -h, --help            show this help message and exit
  -i CIFTI, --cifti CIFTI
                        input CIFTI file
  --gyri GYRI           input gyri textures, typically FreeSurfer gyri.
                        Several may be specified (left, right)
  --gyrus GYRUS         gyrus to extract. Several may be specified. May be a
                        name or a number. If a name is used, the label mapping
                        is expected in the gyri textures header as Gifti
                        'GIFTI_labels_table' attribute.
  -o OUTPUT, --output OUTPUT
                        output gyrus matrix

AimsClosing

-----------------------------------------------------------------------
AimsClosing has been replaced by AimsMorphoMath. Please use it instead.
-----------------------------------------------------------------------

AimsClusterArg


    AimsClusterArg
    --------------

Builds a graph (cluster graph) from an image

Options :

-i | --input <file name (read only): { Volume of FLOAT, Volume of S16, Volume
    of U8 }>  input data

[ -o | --output <string> ]
    output .arg graph file (default: <input>.arg)

[ -g | --graphtype <string> ]
    graph type to produce: c (cluster) or f (cortical folds). default: cluster

[ -t | --trans <string> ]
    transformation matrix to Talairach space (default: none)

[ -c | --connectivity <string> ]
    connectivity type (4xy / 4xz / 4yz / 6 / 8xy / 8xz / 8yz / 18 / 26),
    default: 18

[ -s | --size <S32> ]
    min cluster size (default: 0)

[ -b | --binarize <boolean> ]
    binarize volume (after thresholding) before processing connectivity stuff

[ -l | --lowth <FLOAT> ]
    lower threshold, values under this one are set to zero (background)
    (default: none)

[ -u | --upth <FLOAT> ]
    upper threshold, values above this one are set to zero (background)
    (default: none)

[ -m | --mesh <boolean> ]
    make cluster meshes (default: y)

[ --deciMaxClearance <FLOAT> ]
    maximum clearance of the decimated mesh expected is <clearance> mm
    [default=5.]

[ --deciMaxError <FLOAT> ]
    maximum error distance from the original mesh expected is <error> mm ,
    [default=0.1]

[ --minFacetNumber <U32> ]
    minimum number of facets to allow decimation [default=50]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsCompareSPMtToPrimalSketch


    AimsCompareSPMtToPrimalSketch
    -----------------------------

Select blobs in a PS that are the closest to selected activations in a SPMt -
EXPERIMENTAL. Blobs that are selected are given the activation label in their
'name' attribute

Options :

-p | --primal <file name (read only): Graph>
    PS graph

-s | --spmt <file name (read only): volume of S16>
    spmt image

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsComposeTransformation


    AimsComposeTransformation
    -------------------------

Composes two Aims/anatomist transformations: M1 x M2 [Possibility to use a list
of motions with -i option]

Options :

[ -i <list of string> ]
    M1: 1st input transformation

[ -j <string> ]
    M2: 2nd input transformation [option]

[ -o <string> ]
    output transformation (default: same as 1st input)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsConnectComp


    AimsConnectComp
    ---------------

Extract connected components of a binary data volume

Options :

-i | --input <file name (read only): { Bucket of S16, Bucket of VOID, Volume of
    DOUBLE, Volume of FLOAT, Volume of S16, Volume of S32, Volume of S8, Volume
    of U16, Volume of U32, Volume of U8 }>  input SHORT binary volume

-o | --output <string>
    output labelled connected components volume

[ -c | --connectivity <string> ]
    connectivity  4xy / 4xz / 4yz / 6 / 8xy / 8xz / 8yz / 18 / 26 [default=26]

[ -s | --size <U64> ]
    minimum size of the seeds [default=0]

[ -n <U64> ]
    number of components kept  [default=all]

[ -b <boolean> ]
    force binary mode [default=false]

[ -t | --type <string> ]
    output data type (only applicable to volumes, default: same as input)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsConvexHull


    AimsConvexHull
    --------------

Build triangulation of the convex hull of a list of points

Options :

-i <string>
    file containing 3D points. The file is an ASCII text file. The first line
    should indicate the number of points, the other lines are each one of the
    points, with x, y, z coordinates separated by spaces. Actually the line
    breaks are nor needed but the order of values should be respected.

-o <filename: Mesh of VOID>
    output mesh file

[ -s <boolean> ]
    add symetric directions

[ --ascii <boolean> ]
    output mesh file in ASCII (if supported by the output format)
    [default:binary]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsCorrectionEpi


    AimsCorrectionEpi
    -----------------

Correction of echoplanar distortions in DW MR image
Base on a model of geometric distortion characterized by:
- a scaling S,
- a translation T0,
- a shearing T1

Options :

-t2 <file name (read only): volume of S16>
    T2 image

-dw <file name (read only): volume of S16>
    Diffusion-weighted image

-o <filename: volume of S16>
    Corrected Diffusion-weighted image

[ -divider <S32> ]
    divider for subresolution calculations (default=1)

[ -levels <S32> ]
    number of graylevels in MI calculations (default=64)

[ -smoothing <string> ]
    pdf smoothing deriche/discrete (default=discrete)

[ -sigma <FLOAT> ]
    discrete : gaussian mask size (default=3)
    deriche  : gaussian std dev. (default=3.0mm)

[ -deltaS <FLOAT> ]
    variation of S (default=0.05)

[ -deltaT0 <FLOAT> ]
    variation of T0 (default=1.00)

[ -deltaT1 <FLOAT> ]
    variation of T1 (default=0.01)

[ -error <FLOAT> ]
    tolerance on results (default=0.005)

[ -memMap <boolean> ]
    memory mapping activated (default=no)

[ -parameters <string> ]
    (S,T0,T1) parameter text file name [default=not saved]

[ -verbose <boolean> ]
    show as much information as possible

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsCreateTexture


    AimsCreateTexture
    -----------------

Map a volume on the mesh in the normal direction

Options :

-m | --mesh <file name (read only): Mesh of VOID>
    input_mesh

-v | --volume <string>
    input_volume

-t | --texture | -o <string>
    output_texture

[ --ascii <boolean> ]
    write texture file in ASCII [default=false]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsCurvature2d


    AimsCurvature2d
    ---------------

2D curvature of an intensity image f(x,y) = I

Options :

-i | --input <file name (read only): volume of S16>
    source matrix

-o | --output <filename: volume of FLOAT>
    destination float matrix

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsCurvature3d


    AimsCurvature3d
    ---------------

2D curvature of an intensity image f(x,y) = I

Options :

-i | --input <file name (read only): volume of S16>
    source matrix

-o | --output <filename: volume of FLOAT>
    destination float matrix

[ -g | --gaussian <boolean> ]
    use gaussian curvature [default=mean]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsCylinder


    AimsCylinder
    ------------

2D curvature of an intensity image f(x,y) = I

Options :

-e | --eigen <file name (read only): volume of POINT3DF>
    source eigen vectors file

[ -o | --output <filename: Mesh of VOID> ]
    output mesh file [default=<eigen>.mesh]

[ -m | --mask <file name (read only): volume of U8> ]
    mask on the eigen vectors file

[ -a | --aniso <file name (read only): volume of FLOAT> ]
    anisotropy file to give a length

[ -x <S32> ]
    (x,y,z),(X,Y,Z) defines a sub-volume of interest

[ -y <S32> ]

[ -z <S32> ]

[ -X <S32> ]

[ -Y <S32> ]

[ -Z <S32> ]

[ -t | --topLength <FLOAT> ]
    maximum length of the cylinders [default=3.0]

[ -r | --radius <FLOAT> ]
    radius of the cylinders [default=0.2]

[ -n <S32> ]
    number of division on 2 disk faces of the cylinders [default=6]

[ -l <S32> ]
    number of triangles on each division [default=2]

[ -g <FLOAT> ]
    lower threshold for anisotropy; an eigen vector is valid if its anisotropy
    is greater or equal to <g> [default=0.5]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsDanielssonDist


-------------------------------------------------------------------------
AimsDanielssonDistanceMap  -i[nput] <filein>                             
                           -o[utput] <fileout>                           
                          [-s[ide] <S>] [-h[elp]]                        
-------------------------------------------------------------------------
Danielsson's distance map on a volume                                    
-------------------------------------------------------------------------
     filein  : source volume                                             
     fileout : destination volume                                        
     S       : OUTSIDE, INSIDE, SIGNED [default=SIGNED]                  
-------------------------------------------------------------------------

AimsData2Jpeg


-------------------------------------------------------------------------
AimsData2Jpg -i[nput] <input>                                            
             -o[utput] <output>                                          
             -d[ir] <dir>                                                
            [-s[lice] <slice>]                                           
            [-t[ime] <time> ]                                            
            [-b[egin] <begin>]                                           
            [-e[nd] <end>]                                               
            [-m[in] <minimum>]                                           
            [-M[ax] <maximum>]                                           
            [-c[olormap] <cmap>]                                         
            [-I[ncrement] <inc>]                                         
            [-h[elp]]                                                    
-------------------------------------------------------------------------
 JPEG or PostScript grab on data                                         
 ( S8, U8, S16, U16, S32, U32, FLOAT, DOUBLE )                           
-------------------------------------------------------------------------
     input         : input data file                                     
     output        : output file name for *.jpg or *.ps file             
     dir           : direction of the slice ('x', 'y' or 'z')            
     slice         : index of the slice to grab [default=all slices]     
     time          : time of the volume where to select slice [default=0]
     begin         : start the grab from the beginth slice [default=0]   
     end           : stop the grab at the endth slice [default=dim-1]    
     minimum       : lower float threshold on data                       
     maximum       : upper float threshold on data                       
     cmap          : color map file [default=greyscale]                  
     inc           : increment of slices between two grabs               
                                                                         
     Structure of the cmap file :                                        
                ncolor          |=> number of entries                    
                R G B           |=> 1st color                            
                R G B           |=> 2nd color                            
                . . .                                                    
                . . .                                                    
                . . .                                                    
                . . .                                                    
                R G B           |=> last color                           
-------------------------------------------------------------------------

AimsDicomAnonymize.py

usage: AimsDicomAnonymize.py [-h] [-i INPUT] [-o OUTPUT]

Anonymize input DICOM

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        input DICOM file/directory
  -o OUTPUT, --output OUTPUT
                        output file/directory

AimsDilation

------------------------------------------------------------------------
AimsDilation has been replaced by AimsMorphoMath. Please use it instead.
------------------------------------------------------------------------

AimsDistordDti


-------------------------------------------------------------------------
AimsDistordDti -R[eference] <ref>                                        
               -d[istorded] <dist>                                       
               --S <S>                                                   
               --T0 <T0>                                                 
               --T1 <T1>                                                 
              [--interpolator <interpolator>]                            
              [-h[elp]]                                                  
-------------------------------------------------------------------------
Distord DTI                                                              
-------------------------------------------------------------------------
     ref    : source S16 data                                            
     dist   : distorded S16 data                                         
     S      : magnification                                              
     T0,T1  : translation T = T0 + T1 * x                                
     interpolator : nearest/linear/spline [default=linear]               
-------------------------------------------------------------------------

AimsDtiBck2Vol


------------------------------------------------------------------
AimsDtiBck2Vol -i[nput] <bucket>                                  
               [-o[utput] <dti>]                                  
               [-x <dimx> -y <dimy> -z <dimz>]                    
               [-h[elp]]                                          
------------------------------------------------------------------
Convert a DTI bucket to a FLOAT tensor image                      
------------------------------------------------------------------
     bucket     : input DTI bucket data                           
     dti        : destination FLOAT tensor data [default=bucket]  
     dimx,dimy,                                                   
     dimz       : dimensions of the destination volume            
------------------------------------------------------------------

AimsElevationMap


    AimsElevationMap
    ----------------

Convert 2D data in surface

Options :

-i <file name (read only): { Volume of DOUBLE, Volume of FLOAT, Volume of S16,
    Volume of S32, Volume of S8, Volume of U16, Volume of U32, Volume of U8 }>
    Input 2D short image

-o <filename: Mesh of VOID>
    Output surface

[ -of <filename: Mesh of VOID> ]
    Output flat surface [default: not written]

[ -ob <filename: Mesh of VOID> ]
    Output border surface [default: not written]

[ -s <FLOAT> ]
    Scale factor (intensity)

[ --inv <boolean> ]
    Inverse grey level [default=no]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsErosion

-----------------------------------------------------------------------
AimsErosion has been replaced by AimsMorphoMath. Please use it instead.
-----------------------------------------------------------------------

AimsExtractLabelsFromTexture.py

Usage: AimsExtractLabelsFromTexture.py -i input.gii(.tex) -l old_label(integer) -n new_label(integer) -o output.gii(.tex)

Extract labels from texture.

Options:
  -h, --help            show this help message and exit
  -i FILE, --tex=FILE   input gyri texture
  -l ILABEL, --ilabel=ILABEL
                        input old label
  -n OLABEL, --olabel=OLABEL
                        new label for old label extracted
  -o FILE, --otex=FILE  ouput gyri texture with extracted regions

AimsFiberOversampler


    AimsFiberOversampler
    --------------------

Oversample fibers (number of points

Options :

-i <string>
    Bundle File input

-o <string>
    Bundle File output

[ -points <S32> ]
    number of points to intecalate between 2 points), default = 1

[ -verbose <boolean> ]
    show as much information as possible

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsFileConvert


    AimsFileConvert
    ---------------

Performs file format and data conversion

Options :

-i | --input <file name (read only): { Bucket of DOUBLE, Bucket of DTITENSOR,
    Bucket of FLOAT, Bucket of S16, Bucket of S32, Bucket of U16, Bucket of U32,
    Bucket of VOID, Mesh of VOID, Mesh4 of VOID, Motion of VOID, Segments of
    VOID, Texture of DOUBLE, Texture of FLOAT, Texture of POINT2DF, Texture of
    S16, Texture of S32, Texture of U32, Texture of unsigned integer, Volume of
    CDOUBLE, Volume of CFLOAT, Volume of DOUBLE, Volume of FLOAT, Volume of HSV,
    Volume of POINT3DF, Volume of RGB, Volume of RGBA, Volume of S16, Volume of
    S32, Volume of S8, Volume of U16, Volume of U32, Volume of U8, Volume of
    VECTOR_OF_3_SHORT, Volume of VECTOR_OF_6_FLOAT }>  input data filename to
    convert

-o | --output <string>
    output filename

[ -e | --encoding <S32> ]
    set the data encoding for any output file.
    0 : Binary (default)
    1 : ASCII 
    2 : Base64 binary (for gifti format only)
    3 : Base64 compressed binary (for gifti format only)

[ -n | --normal <boolean> ]
    write normal in output file

[ -r | --rescale <boolean> ]
    rescale output values to amplitude of output format (if output format is an
    integer variant)

[ --imin <DOUBLE> ]
    specify input minimum value for rescaling.

[ --imax <DOUBLE> ]
    specify input maximum value for rescaling.

[ --omin <DOUBLE> ]
    specify output minimum value for rescaling.

[ --omax <DOUBLE> ]
    specify output maximum value for rescaling.

[ --itypelimits <boolean> ]
    uses input type limits instead of dynamic min max to rescale data dynamic.

[ -f | --format <string> ]
    force a specific output format (GIS, NIFTI1, ...) (default: guessed by the
    output filename extension)

[ -t | --type <string> ]
    output data type (only applicable to volumes or textures of scalars,
    default: same as input)

[ -c | --change | --otype <string> ]
    change object type in addition to data type, currently only applicable to
    Bucket of VOID <-> Volume

[ -x | --xdim <U32> ]
    (for output volumes only) forces output volume dimension

[ -y | --ydim <U32> ]
    (for output volumes only) forces output volume dimension

[ -z | --zdim <U32> ]
    (for output volumes only) forces output volume dimension

[ --orient <string> ]
    change/force output volume voxels orientation on disk (if the output format
    supports it), with different syntaxes:
    --orient "flipx yflip": flips orientations of x and y axes.
    --orient neuro or --orient neurological or --orient left-to-right: force
    neuro orientation.
    --orient radio or --orient radiological or --orient right-to-left: force
    radio orientation.
    --orient "-1 1 -1": set a flip matrix flipping x and z axes.
    --orient "-1 0 0  0 1 0  0 0 -1": same by specifying the full rotation
    matrix.
    --orient "-1 0 0 255  0 1 0 0  0 0 -1 123  0 0 0 1": same by specifying the
    full 4x4 matrix.
    By default, all orientation matrices are applied relatively to the current
    voxels orientation. To set absolute matrices (from the AIMS conventional
    orientation), specify "abs:" before the matrix. Ex:
    --orient "abs: -1 1 -1"
    --orient "abs: -1 0 0 255  0 1 0 0  0 0 -1 123  0 0 0 1"

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsFileInfo


    AimsFileInfo
    ------------

Give information about a data file (any file Aims can read)

Options :

-i | --input <string>
    input data file

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose | -v [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsFlip


    AimsFlip
    --------

Image flip

Options :

-i | --input <string>
    input image to flip

-o | --output <string>
    output flipped image

-m <string>
    flip image XX, YY, ZZ, XXYY, XXZZ, YYZZ, XXYYZZ, or flip axes : XY, XZ, YZ 

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsFoldArgAtt


    AimsFoldArgAtt
    --------------

Builds cortical folds graph attributes - replaces VipFoldArgAtt

Options :

-i <file name (read only): volume of S16>
    skeleton image

-g <file name (read only): Graph>
    fold graph

[ -o <filename: Graph> ]
    output fold graph [default: input]

[ -m <string> ]
    transformation to Talairach [default: none]

[ -n | --nomesh <boolean> ]
    don't generate meshes

[ --smoothType <string> ]
    mesh smoothing alorithm's type (if meshes are generated) : laplacian or
    lowpass  [default=lowpass]

[ --apc <string> ]
    set AC/PC/IH points in graph from a .APC file [default: don't set them]

[ -li <S16> ]
    'inside' label on skeleton image [default: 0]

[ -lo <S16> ]
    'outside' label on skeleton image [default: 11]

[ --graphversion <string> ]
    output graph version [default: 4.6]

[ --threads <S32> ]
    limit threads usage. code: 0: one thread per CPU; 1: mono-threaded; n>0:
    use exactly n threads; -n: use one thread per CPU, up to n max. Default: 0.
    Note: no effect on Windows, threading is disabled

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsFoldsGraphOverSegmentation.py

Usage: AimsFoldsGraphOverSegmentation.py [options]

Split fold nodes that are too big into smaller pieces

Options:
  -h, --help            show this help message and exit
  -i GRAPH_NAME, --input=GRAPH_NAME
                        input graph
  -o OUTPUT_GRAPH_NAME, --output=OUTPUT_GRAPH_NAME
                        output graph
  -l LENGTH, --length=LENGTH
                        target length of split pieces [default: 20mm]
  -m MINSIZE, --minsize=MINSIZE
                        minimum size (in voxels) of split pieces [default: 50]

AimsFoldsGraphThickness.py

Usage: AimsFoldsGraphThickness.py [options]

Processing of Cortical thickness attributes in Cortical Folds Graph

Options:
  -h, --help            show this help message and exit
  -i GRAPH_NAME, --input=GRAPH_NAME
                        input graph
  -c HEMI_CORTEX_NAME, --cortex=HEMI_CORTEX_NAME
                        segmented cortex volume (LCR + Grey)
  -g GW_INTERFACE_NAME, --gw=GW_INTERFACE_NAME
                        segmented cortex volume (Grey, White, LCR)
  -w WHITE_MESH_NAME, --white=WHITE_MESH_NAME
                        white mesh
  -l HEMI_MESH_NAME, --lcr=HEMI_MESH_NAME
                        hemi mesh (Grey-LCR interface)
  -o OUTPUT_GRAPH_NAME, --output=OUTPUT_GRAPH_NAME
                        output graph
  -m OUTPUT_MID_INTERFACE_NAME, --mid=OUTPUT_MID_INTERFACE_NAME
                        output mid_interface (optional)
  -s OUTPUT_LCR_GREY_WHITE_NAME, --savelgw=OUTPUT_LCR_GREY_WHITE_NAME
                        output volume of lcr, grey and white matter for the
                        use of computing thickness (optional)
  -v VORONOI, --voronoi=VORONOI
                        sulci voronoi diagram, optional, recalculated if not
                        provided

AimsFovSplit


    AimsFovSplit
    ------------

Premier program  rats

Options :

-i <list of string>
    input files (1 minimum)

[ -o <vector of string> ]
    output file names (give as many as you want of rats if the automatic names
    do not suit you)

[ -r <U32> ]
    Nbre de rat [default: number of output file names, of by default : 4 rats] 

[ -m <S32> ]
    Taille minimale des composantes connexes [default: 1000] 

[ -t <FLOAT> ]
    Seuil initial de recherche [default: 20000] 

[ -p <FLOAT> ]
    Pas de d�r�ent du seuil [default: 10] 

[ --binary <boolean> ]
    Image used to split is almost binary

[ -d <string> ]
    dirname

[ -u <boolean> ]
    perform unlink

[ -a <string> ]
    attenuation file name

[ --a2split <boolean> ]
    use attenuation file to split

-gcA <vector of FLOAT>
    Force first gravity center(optional) : must set others too

-gcB <vector of FLOAT>
    Force second gravity center(optional) : must set others too

-gcC <vector of FLOAT>
    Force third gravity center(optional) : must set others too

-gcD <vector of FLOAT>
    Force fourth gravity center(optional) : must set others too

[ -verbose <boolean> ]
    yields some more info

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)

bin/AimsFovSplit: user interruption

AimsFrontDistanceMap


    AimsFrontDistanceMap
    --------------------

Chamfer distance map by front propagation
Propagation starts from voxels with any value not in (<forbidden>, <domain>)
and propagates inside voxels with value <domain>. All voxel values different
from <forbidden> and <domain> are considered to be the seed (zero distance)

Options :

-i | --input <file name (read only): { Bucket of FLOAT, Bucket of S16, Bucket
    of VOID, Volume of FLOAT, Volume of S16 }>  source label data

-o | --output <string>
    output distance map

[ -d | --domain <DOUBLE> ]
    valid domain label where to propagate the diagram [default=0]

[ -f | --forbidden <DOUBLE> ]
    forbidden domain [default=-1]

[ -x | --xmask <S32> ]
    X size of the distance mask [default=3]

[ -y | --ymask <S32> ]
    Y size of the distance mask [default=3]

[ -z | --zmask <S32> ]
    Z size of the distance mask [default=3]

[ -F | --factor <FLOAT> ]
    chamfer multiplication factor [default=50]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsGTMDump


----------------------------------------------------------------
AimsGTMDump -i[nput] <filein>                                   
            -h[elp]                                             
----------------------------------------------------------------
 Dump Gtm                                                       
----------------------------------------------------------------
     filein    : origin Roi file (arg format)                   
----------------------------------------------------------------

AimsGaussianSmoothing


    AimsGaussianSmoothing
    ---------------------

3D Deriche's recursive gaussian smoothing filter

Options :

-i | --input <file name (read only): { Volume of DOUBLE, Volume of FLOAT,
    Volume of S16, Volume of S32, Volume of S8, Volume of U16, Volume of U32,
    Volume of U8 }>  source volume

-o | --output <string>
    destination volume

[ -x | --xsigma <FLOAT> ]
    X standard deviation of the gaussian filter [default=largest voxel size]

[ -y | --ysigma <FLOAT> ]
    Y standard deviation of the gaussian filter [default=largest voxel size]

[ -z | --zsigma <FLOAT> ]
    Z standard deviation of the gaussian filter [default=largest voxel size]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsGaussianSmoothing1d


    AimsGaussianSmoothing1d
    -----------------------

1D Deriche's recursive gaussian smoothing filter.

Options :

-i | --input <string>
    Source volume

-o | --output <string>
    Destination volume

-d | --direction <string>
    Direction of smoothing: x, y, z

[ -s | --sigma <FLOAT> ]
    Standard deviation of the gaussian function
    [default = corresponding voxel size]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsGetTransformation.py

Usage: AimsGetTransformation.py [options]

extract an affine transformation information in an object header into a
transformation file

Options:
  -h, --help            show this help message and exit
  -i FILE, --input=FILE
                        object to get transformation from (volume, mesh, etc).
  -o TRMFILE, --output=TRMFILE
                        output transformation file (*.trm)
  -n TRANSNUM, --number=TRANSNUM
                        get transformation information as the n-th
                        transformation. Default: -1, last one in list
  -d DESTINATION, --destination=DESTINATION
                        set destination referential name/UUID. Default: try to
                        get it from the referentials info of the input file
                        header
  -s SOURCE, --source=SOURCE
                        set source referential name/UUID. Default: try to get
                        it from the referential info of the input file header

AimsGraphComplete


    AimsGraphComplete
    -----------------

Completes missing attributes in graphs (cortical folds graphs generally)

Options :

-i | -input <file name (read only): Graph>
    input graph

[ -o | -output <filename: Graph> ]
    output (completed) graph [default=input]

[ --dversion <string> ]
    set data graph version

[ --mversion <string> ]
    set model graph compatibility version

[ --forceversion <boolean> ]
    force data/model graph versions [default: only if newer]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsGraphConvert


    AimsGraphConvert
    ----------------

Performs graph storage conversion or volume-S16 labels volume to graph
conversion

Options :

-i | -input <string>
    input data graph

[ -o | -output <string> ]
    output data graph (default: same as input)

[ -b | -basename <string> ]
    directory where to put sub-data in (default: <input>.data)

[ -g | -global <boolean> ]
    save sub-objects in 'global' mode (1 file for all objects of same type)

[ -l | -local <boolean> ]
    save sub-objects in 'local' mode (each object with a specific file)
    (contradictory with -g)

[ -c | -copy <string> ]
    copy attribute (use with -d)

[ -d | -dest <string> ]
    destination attribute (for use with -c)

[ -s | -syntax <string> ]
    syntax of elements involved by copy operations (use with -c and -d)
    [default: no filtering]

[ --volume <boolean> ]
    convert buckets to volume of labels

[ --bucket <boolean> ]
    convert volumes of labels to buckets

[ --roi <boolean> ]
    Output graph will be a roi graph, and all unnamed regions will be named by
    their roi label

[ --substitution <string> ]
    Graph substitution file for syntax and label

[ --labels <string> ]
    Substitution file for label's name

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsGraphExtractTransformation


    AimsGraphExtractTransformation
    ------------------------------

Extracts the Talairach transformation in a graph file and write it as an
Aims/Anatomist transformation file

Options :

-i | -input <string>
    input data graph

[ -o | -output <string> ]
    output transformation (default: <input>TOtalairach.trm)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsGraphMerge


    AimsGraphMerge
    --------------

Merge 2 graphs (cortical folds graphs generally)

Options :

-i | -input1 <file name (read only): Graph>
    input graph1

-k | -key <string>
    matching key

-j | -input2 <file name (read only): Graph>
    input graph2

[ -o | -output <filename: Graph> ]
    output (merge) graph [default=input]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsGraphMesh


    AimsGraphMesh
    -------------

Performs graph storage conversion and sub-buckets meshing
This command is an improved version of AimsGraphConvert

Options :

-i | -input <file name (read only): Graph>
    input data graph

[ -o | -output <filename: Graph> ]
    output data graph (default: same as input)

[ -b | -basename <string> ]
    directory where to put sub-data in (default: <output>.data)

[ -g | -global <boolean> ]
    save sub-objects in 'global' mode (1 file for all objects of same type)

[ -l | -local <boolean> ]
    save sub-objects in 'local' mode (each object with a specific file)
    (contradictory with -g)

[ -m | -mesh <vector of string> ]
    mesh some objects into the given attribute
    Needs at least one -mb option (default: aims_Tmtktri)

[ -mb | -meshbucket <vector of string> ]
    mesh buckets of given attribute (experts manips). Needs also a -m option.
    Specify several -mb <attrib> to mesh several buckets(default: all)

[ -f <U32> ]
    minimum number of facets to mesh (default 50)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsGraphTransferLabels


    AimsGraphTransferLabels
    -----------------------

Transfers labelling from a buckets graph to another graph.
Graph structures don't need to match, transfer is based on a Voronoi diagram

Options :

-i | --input1 <file name (read only): Graph>
    input graph to set labels into

-j | --input2 <file name (read only): Graph>
    input labelled graph to take labels from

[ -o | --output <filename: Graph> ]
    output labelled graph [default=input]

[ -l | --label <string> ]
    label attribute [default=name]

[ -v | --voronoi <filename: volume of S16> ]
    output voronoi diagram (in input2 space) [default=not saved]

[ -m | --map <string> ]
    output labels map file [default=not saved]

[ -s | --samespace <boolean> ]
    force same space for both graphs (ignore Talairach transforms)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsGyriTextureCleaningIsolatedVertices.py

usage: AimsGyriTextureCleaningIsolatedVertices.py [-h] gyriseg mesh ogyriseg

-------------------------------------------------------------------
Clean a label AimsTimeTexture from isolated vertices
-------------------------------------------------------------------

positional arguments:
  gyriseg     input gyri texture
  mesh        input mesh
  ogyriseg    gyri texture with one connected component per gyrus

optional arguments:
  -h, --help  show this help message and exit

AimsHJEvolution2d


--------------------------------------------------------------------------
AimsHJEvolution2d -i[nput]   <filein>                                     
                  -o[output] <fileout>                                    
                  -e[poch]   <epoch>                                      
                  [-t[ime]   <timestep>]                                  
                  [-f[0]     <F0>]                                        
                  -F[1]      <F1>                                         
                  [-s[tep]   <savingstep>]                                
                  [-u[radius] <tuberadius>]                               
                  [-m[orphology] <typeMorpho>]                            
                  [-h[elp]]                                               
--------------------------------------------------------------------------
2D Hamilton-Jacobi evolution of a binary short image f(x,y)               
Fast tubular method                                                       
--------------------------------------------------------------------------
  filein    : input SHORT binary data                                     
  fileout   : prefix name for output SHORT data                           
  epoch     : number of evolving iterations to proceed                    
  timestep  : time step in seconds [default=0.1]                          
  F0,F1     : speed function F = F0 + F1.K [default F0=-1.0 / F1=-1.0]    
              F0<0 : erosion  / F0>0 : dilation                           
  savingtep : number of time iterations between 2 backups [default=1]     
  uradius   : radius of the evolving tube [default=12]                    
  typeMorpho: type of morphologic evolution                               
                   0 -> -F0.||DPhi||                                      
                   1 -> -F0.||DPhi||.dist(x,y)                            
                   2 -> -F0.||DPhi||.(1.0 + 0.5 * dist(x,y))              
--------------------------------------------------------------------------

AimsHJEvolution3d


--------------------------------------------------------------------------
AimsHJEvolution3d  -i[nput] <filein>                                      
                   -o[output] <fileout>                                   
                  [-d[istmap] <filedist>                                  
                   -e[poch] <epoch>                                       
                  [-t[ime] <timestep>]                                    
                  [-f[0] <F0>]                                            
                   -F[1] <F1>                                             
                  [-s[tep] <savingstep>]                                  
                  [-u[radius] <tuberadius>]                               
                  [-c[urvature] <typeCurv>]                               
                  [-m[orphology] <typeMorpho>]                            
                  [-h[elp]]                                               
--------------------------------------------------------------------------
3D Hamilton-Jacobi evolution of a binary short image f(x,y,z)             
Fast tubular method                                                       
--------------------------------------------------------------------------
  filein    : input SHORT binary volume                                   
  fileout   : prefix name for output SHORT volumes                        
  filedist  : distance map volume                                         
  epoch     : number of evolving iterations to proceed                    
  timestep  : time step in seconds [default=0.1]                          
  F0,F1     : speed function F = F0 + F1.K [default F0=-1.0 / F1=-1.0]    
              F0<0 : erosion  / F0>0 : dilation                           
  savingtep : number of time iterations between 2 backups [default=1]     
  uradius   : radius of the evolving tube [default=12]                    
  typeCurv  : mean, gaussian, mean-gaussian, min, max                     
                                            [default=mean-gaussian]       
  typeMorpho: type of morphologic evolution                               
                   0 -> -F0.||DPhi||                                      
                   1 -> -F0.||DPhi||.dist(x,y,z)                          
                   2 -> -F0.||DPhi||.(1.0 + 0.5 * dist(x,y,z))            
--------------------------------------------------------------------------

AimsHippocampicReferential


    AimsHippocampicReferential
    --------------------------

Transformation to hippocampic referential

Options :

-o <string>
    Output motion file

--ac <vector of FLOAT>
    Anterior commissure (mm)

--pc <vector of FLOAT>
    Posterior commissure (mm)

--ih <vector of FLOAT>
    Inter hemispheric point (mm)

[ --angle <FLOAT> ]
    rotation angle in degrees (default 30°)

[ --axis <string> ]
    rotation axis 'x', 'y' or 'z' (default x)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsIcmSpaghetti


-------------------------------------------------------------------------
AimsIcmSpaghetti -i[nput] <input>                                        
                 -o[utput] <output>                                      
                [-a[lpha] <alpha>]                                       
                [-m[odifAngle] <modifAngle>]                             
                [-n[eighborAngle] <neighborAngle>]                       
                [-s[ampling] <sampling>]                                 
                [-M[axIter] <iteration>]                                 
                [-h[elp]]                                                
-------------------------------------------------------------------------
 Regularization of the tensor maps with a Spaghetti Markov Field         
-------------------------------------------------------------------------
    input         : bucket of dtitensor to be regularized                
    output        : result of the regularization                         
    alpha         : energy balancing  [default=1.0]                      
                    V = V(spaghetti) + alpha x V(attachment)             
    modifAngle    : maximum angle in degrees between the direction of a  
                    neighbor of a voxel and the spin of that voxel       
                    [default=45deg]                                      
    neighborAngle : maximum angle in degrees beetween 2 spins to be      
                    considered in the same fiber                         
                    [default=46deg]                                      
    sampling      : minimum number of discrete unit vectors uniformly    
                    distributed on a unit sphere                         
                    [default=162]                                        
    iteration     : stop the ICM after a maximum number of iterations    
                    [default=30]                                         
-------------------------------------------------------------------------

AimsIcmSpaghettiN


-------------------------------------------------------------------------
AimsIcmSpaghettiN -i[nput] <input>                                       
                  -o[utput] <output>                                     
                 [-a[lpha] <alpha>]                                      
                 [-m[odifAngle] <modifAngle>]                            
                 [-n[eighborAngle] <neighborAngle>]                      
                 [-s[ampling] <sampling>]                                
                 [-M[axIter] <iteration>]                                
                 [--neighbor <nneighbor>]                                
                 [-h[elp]]                                               
-------------------------------------------------------------------------
 Regularization of the tensor maps with a Spaghetti Markov Field         
-------------------------------------------------------------------------
    input         : bucket of dtitensor to be regularized                
    output        : result of the regularization                         
    alpha         : energy balancing  [default=1.0]                      
                    V = V(spaghetti) + alpha x V(attachment)             
    modifAngle    : maximum angle in degrees between the direction of a  
                    neighbor of a voxel and the spin of that voxel       
                    [default=45deg]                                      
    neighborAngle : maximum angle in degrees beetween 2 spins to be      
                    considered in the same fiber                         
                    [default=46deg]                                      
    sampling      : minimum number of discrete unit vectors uniformly    
                    distributed on a unit sphere                         
                    [default=162]                                        
    iteration     : stop the ICM after a maximum number of iterations    
                    [default=30]                                         
    nneighbor     : number of neighbor by semi-conic neighborhood        
                    [default=all]                                        
-------------------------------------------------------------------------

AimsIcosaList


-------------------------------------------------------------------------
AimsIcosaList  -d[irection] <dir>                                        
               -o[utput] <output>                                        
               [-e[psilon] <eps>]                                        
               [-a[ll]]                                                  
               [-h[elp]]                                                 
-------------------------------------------------------------------------
 Output a file with coordinates of discrete spheric distribution         
-------------------------------------------------------------------------
     dir           : number of discrete directions                       
     output        : output ASCII file                                   
     all           : all directions (+d and -d)                          
                     (useful for DTI where +d and -d are equivalent      
     eps           : error on dot product (+d).(-d) [default=1e-6]       
-------------------------------------------------------------------------

AimsImageGLBlobStats

Here we go !

    AimsImageGLBlobStats
    --------------------

Compute every scale and corresponding grey-level blob measurements from an
image

Options :

-i <string>
    input data

-m <string>
    mask

[ -t1 <FLOAT> ]
    scale min (default=1.0)

-t2 <FLOAT>
    scale max

-p <string>
    stats file name pattern

-s <S32>
    smoother (0 : Gaussian, 1 : diffusion)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsImagePrimalSketch


    AimsImagePrimalSketch
    ---------------------

ScaleSpace d'une image au format FLOAT

Options :

-i | --input <string>
    inputImage

-m | --mask <string>
    mask

-os | --output-scales <string>
    output scalespace filename

-ob | --output-blobs <string>
    output blobs filename

[ -t1 | --scalemin <FLOAT> ]
    minimum scale (default=1.0)

-t2 | --scalemax <FLOAT>
    maximum scale

[ -s | --smoother <S32> ]
    smoother (0 : Gaussian, 1 : diffusion; default=0)

[ -dt | --deltat <FLOAT> ]
    time step (for diffusion only; default=0.1)

[ -f | --stats <string> ]
    name of file containing statistics for blob measurements normalisation

[ -sj | --subject <string> ]
    subject name (default : inputImage)

[ -og | --graph <string> ]
    primal sketch graph

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsImageScaleSpace


    AimsImageScaleSpace
    -------------------

ScaleSpace d'une image...

Options :

-i | --input <string>
    inputImage

-o | --output <string>
    output filename pattern

-tm | --scalemax <FLOAT>
    maximum scale

-s | --smoother <S32>
    smoother (0 : Gaussian, 1 : diffusion

-dt | --deltat <FLOAT>
    time step

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsImageSmoothing


    AimsImageSmoothing
    ------------------

Image smoothing by diffusion or recursive filtering

Options :

-i | --input <string>
    input Image

-o | --output <string>
    output Image

-t | --scale <FLOAT>
    scale

-s | --smoother <S32>
    smoother (0 : Gaussian, 1 : isotropic diffusion, 2 : Perona-Malik)

[ -dt | --deltat <FLOAT> ]
    time step (diffusion only; default=0.1)

[ -k | --gradient <FLOAT> ]
    gradient bound (0-1), Perona-Malik only, default=0.98

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsInflate


    AimsInflate
    -----------

Gonflement d'une surface (tri ou mesh)

Options :

-i | --input <string>
    input

[ -t | --time <S32> ]
    evolution time

-o | --output <string>
    output filename

[ -Kn | --Knormal <FLOAT> ]
    normal force weight (default=0.01)

[ -Ksp | --Kspring <FLOAT> ]
    spring force weight (default=0.01)

[ -Ksm | --Ksmooth <FLOAT> ]
    smoothing force weight (default=0.5)

[ -B | --Bound <FLOAT> ]
    bound for the force computation (default=5000.0)

[ -S | --Sequence <boolean> ]
    to save the inflating sequence

-c | --curvature <string>
    mean curvature file name

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsInvertTransformation


    AimsInvertTransformation
    ------------------------

Inverts an Aims/anatomist transformation

Options :

-i <string>
    input transformation

[ -o <string> ]
    output (inverted) transformation (default: <input>_inverted.trm)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsKMeans


-------------------------------------------------------------------------
AimsKMeans	-f[ile]  <data file>
             -g[ile2] <data file>
             -i[nput] <image>
             -o[utput]
             -n[umber]
             [-h[elp]]
-------------------------------------------------------------------------
	Image des classes produite par le kmeans
-------------------------------------------------------------------------
     file        : nom fichier containing the classification             
     file2       : nom fichier des donnees initiales                     
     input       : nom image segmentee                                   
     fileout     : nom image sortie	des classes
     number      : number of vectors                                     
-------------------------------------------------------------------------

AimsKMeansImageSegmentation


    AimsKMeansImageSegmentation
    ---------------------------

K means based automatic segmentation

Options :

-i <string>
    dynamic series file

-o <string>
    fileout segmentation image filename

-c <S32>
    number of classes

-r <S32>
    number of runs

[ -m <string> ]
    input mask of organism of interest (example: brain mask)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsLabelSelector


    AimsLabelSelector
    -----------------

Selects ROI labels from a nomenclature
(to be used as input for ROI and morphometry commands)

Options :

[ -m | --model <string> ]
    Load a model

[ -n | --nomenclature | --hierarchy <string> ]
    Load a nomenclature hierarchy

[ -p | --presel <string> ]
    Load a pre-made selection

[ -b | --batch <boolean> ]
    Batch mode: process the input selection/model if possible and immediately
    outputs a selection without user interaction

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsLabels2Tex


    AimsLabels2Tex
    --------------

Compute label close to mesh and build texture file

Options :

-i | --input <string>
    input Label volume

-m | --mesh <file name (read only): Mesh of VOID>
    input mesh

-o | --output <string>
    texture output

[ -height <S32> ]
    cylinder half height (voxels) [default=1]

[ -radius <S32> ]
    cylinder radius (voxels) [default=1]

[ -mode <S32> ]
    cylinder direction (1:interior, 2:exterior, 3:both) [default=3]

[ -b <string> ]
    brain mask file [default=no brain mask]

[ --ascii <boolean> ]
    write texture file in ASCII [default=false]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsLightenAtlas


    AimsLightenAtlas
    ----------------

Lighten anatomical probabilistic atlas

Options :

-i <string>
    Probabilistic atlas image with one region per frame

-o <string>
    Lightened atlas image

[ -s <string> ]
    Sum of the lightened atlas image

[ -r <FLOAT> ]
    Radius around a point in the structure within which a point with a 1
    probability
    to belong to the structure is supposed to exist (default : 8 mm)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsLinearComb

WARNING: AimsLinearComb is obsolete. Please use cartoLinearComb.py instead.


------------------------------------------------------------------
AimsLinearComb  -i <i1>  [-a <num1>] [-b <den1>]                  
               [-j <i2>  [-c <num2>] [-d <den2>]]                 
               [-e <cst>]                                         
                -o[utput] <fileout>                               
               [-t[ype] <datatype>                                
               [-h[elp]]                                          
------------------------------------------------------------------
Linear combination a.I1/b + c.I2/d  + e                           
                                                                  
Note : a,b,c,d,e must be real                                     
------------------------------------------------------------------
     i1      : first data (volume or texture)                     
     num1    : multiplicative coefficient for the first data [1.0]
     den1    : divisor coefficient for the first data [1.0]       
     i2      : second data (volume or texture)                    
               (if none, linear combination a.I1/b)  
     num2    : multiplicative coefficient for the second data[1.0]
     den2    : divisor coefficient for the second data [1.0]      
     cst     : constant offset value [default=0.0]                
     fileout : destination data                                   
     datatype: data type of the destination volume/texture (S16, U8, ...) 
               [default=type of in1]                              
               For texture, i1, i2 and fileout must have the same type
------------------------------------------------------------------

AimsMIRegister


    AimsMIRegister
    --------------

Registration according to Mutual Information Method

Options :

-r | --reference <string>
    source reference volume

-t | --test <string>
    source test volume to register)

[ -cr <S32> ]
    Channel of multi-channel reference image to use during registration
    estimation
    Possible types and values:
    type : RGB or RGBA
    values: 0=red, 1=green, 2=blue, 3=alpha, 4=norm
    
    type : HSV
    values: 0=hue, 1=saturation, 2=value, 4=norm
    
    [default is set to norm]
    

[ -ct <S32> ]
    Channel of multi-channel test image to use during registration estimation
    Possible types and values:
    type : RGB or RGBA
    values: 0=red, 1=green, 2=blue, 3=alpha, 4=norm
    
    type : HSV
    values: 0=hue, 1=saturation, 2=value, 4=norm
    
    [default is set to same value as reference channel]
    

[ --dir <filename: AffineTransformation3d> ]
    test_TO_ref: output transfomation filename [default=<test>_TO_<ref>.trm]

[ --inv <filename: AffineTransformation3d> ]
    ref_TO_test: output transfomation filename [default=<ref>_TO_<test>.trm]

[ -l | --logger <string> ]
    output log file

[ --serialnum <S32> ]
    number of the frame to consider for ref [default 0], relevant for dynamic
    series ref images

[ --Tx <FLOAT> ]
    Init Translaction coord [default=0.]

[ --Ty <FLOAT> ]
    Init Translaction coord [default=0.]

[ --Tz <FLOAT> ]
    Init Translaction coord [default=0.]

[ --dTx <FLOAT> ]
    Increment for variable Tx [default=heuristics in code]

[ --dTy <FLOAT> ]
    Increment for variable Ty [default=heuristics in code]

[ --dTz <FLOAT> ]
    Increment for variable Tz [default=heuristics in code]

[ --Rx <FLOAT> ]
    Init Rotation coord [default=0.]

[ --Ry <FLOAT> ]
    Init Rotation coord [default=0.]

[ --Rz <FLOAT> ]
    Init Rotation coord [default=0.]

[ --dRx <FLOAT> ]
    Increment for variable Rx [default=heuristics in code]

[ --dRy <FLOAT> ]
    Increment for variable Ry [default=heuristics in code]

[ --dRz <FLOAT> ]
    Increment for variable Rz [default=heuristics in code]

[ --interpolation <string> ]
    interpolation  nearest/linear/spline [default=linear]

[ --optimization <string> ]
    optimaizer  powell/random/single [default=powell]
    single --> get a one shot evaluation
    random --> sample cost value in a given area
    powell --> cost minimization with powell algorithm

[ --pdfcalc <string> ]
    Pdf calculus mode : direct ou pv [default=pv]

[ --gcinit <string> ]
    Init with GravCenter: yes/no [default=yes]

[ --index <string> ]
    index to be optimized mi/cr [default=mi]
    Mutual Information --> mi
    Correlation Ratio  --> cr

[ --refstartpyr <S32> ]
    level of the multiresolution optimization:
    start resolution level for ref

[ --refendpyr <S32> ]
    level of the multiresolution optimization:
    end resolution level for ref

[ --teststartpyr <S32> ]
    level of the multiresolution optimization:
    start resolution level for tes

[ --testendpyr <S32> ]
    level of the multiresolution optimization:
    end resolution level for tes

[ --pays_size <S32> ]
    Half size the volume generated if optimization=other activated

[ --graylevel <S32> ]
    numb of classes in histogram pdf estimation [default=64]

[ --masksize <S32> ]
    size of the gaussian convolution mask in pdf estimation for Mutual
    Information [default=5]

[ --error <FLOAT> ]
    tolerance on results [default=0.01]

[ --threshref | --seuilref <FLOAT> ]
    relative thresh applied prior to grav cent estimation

[ --threshtest | --seuiltest <FLOAT> ]
    relative thresh applied prior to grav cent estimation

[ --generatecurve | -g <boolean> ]
    generate curve file with default name 'courbe' [default=true]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsManualBiasCorrection


------------------------------------------------------------------------- 
AimsManualBiasCorrection -i[nput]  <filein>                               
             -o[utput] <fileout>                                          
             -d[irection] <direction : x, y, or z>                        
             -f[irst] <first slice value>                                  
             -l[ast] <last slice value>                                     
------------------------------------------------------------------------- 
Morphological dilation                                                    
------------------------------------------------------------------------- 
     filein   : source volume                                             
     fileout  : destination volume                                        
     direction: direction of bias correction : x axis, y axis, ou z axis  
     f        : first slice white matter level                            
     l        : last slice white matter level                             
-------------------------------------------------------------------------

AimsMask


    AimsMask
    --------

Mask an image with another one

Options :

-i <string>
    origin file

-o <string>
    output file

-m <string>
    mask

[ --inv <boolean> ]
    use inverse mask image (default=no)

[ -d <string> ]
    Default values for masked pixels [default=0]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMaskPhantom


----------------------------------------------------------------
AimsMaskPhantom  -i[nput] <filein>                              
                [-o[utput] <fileout>]                           
                [--centerX <cx>]                                
                [--centerY <cy>]                                
                [--centerZ <cz>]                                
                [--radius <R>]                                  
                [--withSphere]                                  
                 --bandX <bx>                                   
                 --bandW <bw>                                   
                [-r[eader] <reader>]                            
                [-h[elp]]                                       
----------------------------------------------------------------
Special masking of DTI Phantom for Anne Darquie                 
----------------------------------------------------------------
  filein        : origin file                                   
  fileout       : output file [default=filein]                  
  cx, cy, cz, R : center and radius of the sphere for masking   
                  Eddy current [default=no masking]             
  --withSphere  : mask Eddy Current with sphere [default=no]    
  bx, bw        : x-coordinate and width of the band to mask the
                  air buble                                     
----------------------------------------------------------------

AimsMassCenter


    AimsMassCenter
    --------------

Computes position of the mass center of the image

Options :

-i | --input <file name (read only): { Volume of DOUBLE, Volume of FLOAT,
    Volume of S16, Volume of S32, Volume of S8, Volume of U16, Volume of U32,
    Volume of U8 }>  input data

[ -b | --binary <boolean> ]
    consider input image as binary data

[ -r | --roi <string> ]
    input ROI file (either ROI graph or image)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose | -v [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeanCurvFlow


--------------------------------------------------------------------------
AimsMeanCurvFlow  -i[nput]   <filein>                                     
                  -o[output] <fileout>                                    
                  -e[poch]   <epoch>                                      
                  -F[1]      <F1>                                         
                 [-t[ime]   <timestep>]                                   
                 [-s[tep]   <savingstep>]                                 
                 [-u[radius] <tuberadius>]                                
                 [-c[urvature] <typeCurv>]                                
                 [-r[eader] <reader>]                                     
                 [-h[elp]]                                                
--------------------------------------------------------------------------
3D Hamilton-Jacobi evolution of a binary short image f(x,y,z)             
Fast tubular method - Mean Curvature Flow                                 
       Ut = - F1.K.||DU||                                                 
--------------------------------------------------------------------------
  filein    : input SHORT binary volume                                   
  fileout   : prefix name for output SHORT volumes                        
  epoch     : number of evolving iterations to proceed                    
  timestep  : time step in seconds [default=0.1]                          
  F1        : speed function F = F1.K [default F1=-1.0]                   
  savingtep : number of time iterations between 2 backups [default=1]     
  uradius   : radius of the evolving tube [default=12]                    
  typeCurv  : mean, gaussian, mean-gaussian, min, max                     
                                            [default=mean-gaussian]       
--------------------------------------------------------------------------

AimsMedianSmoothing


    AimsMedianSmoothing
    -------------------

Median filter smoothing

Options :

-i | --input <file name (read only): { Volume of DOUBLE, Volume of FLOAT,
    Volume of RGB, Volume of RGBA, Volume of S16, Volume of S32, Volume of S8,
    Volume of U16, Volume of U32, Volume of U8 }>  source volume

-o | --output <string>
    destination volume

[ -x | --dx <S16> ]
    X size of the filter mask [default=3]

[ -y | --dy <S16> ]
    Y size of the filter mask [default=3]

[ -z | --dz <S16> ]
    Z size of the filter mask [default=3]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMerge


    AimsMerge
    ---------

Merge a volume and a byte label volume

Options :

-i | --input <string>
    origin file

-o | --output <string>
    output file

-M | --Mask <string>
    mask file (int voxel type)

-m | --mode <string>
    mode that can be:
    sv --> same values, put value of the mask where the mask is non-zero;
    oo --> one to one, put `-v' where the mask is `-l';
    ao --> all to one, put `-v' where the mask is non-zero;
    om --> one to maximum plus 1, put max(input)+1 where mask is `-l';
    am --> all to maximum plus 1, put max(input)+1 where mask is non-zero.

[ -l | --label <S32> ]
    only label to get into account

[ -v | --value <DOUBLE> ]
    replacement value

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMerge2Rgb


    AimsMerge2Rgb
    -------------

Merge 3 AimsData<byte> files to an AimsData<AimsRGB>

Options :

-r <string>
    input U8 data R channel

-g <string>
    input U8 data G channel

-b <string>
    input U8 data B channel

-o <string>
    output data

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMergeLabel


    AimsMergeLabel
    --------------

Merge several label data into a new label data

Options :

-i <list of string>
    input label data filename list

[ -b <list of S16> ]
    background labels for label data (default=-1)

-o <string>
    output label data filename

[ -bo <S16> ]
    background label for output label data (default=-1)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMergeLabelsFromTexture.py

Usage: AimsMergeLabelsFromTexture.py -i input.gii(.tex) -l old_label(integer) -n new_label(integer) -o output.gii(.tex)

Change/Merge labels from texture.

Options:
  -h, --help            show this help message and exit
  -i FILE, --tex=FILE   input gyri texture
  -l ILABEL, --ilabel=ILABEL
                        input old label
  -n OLABEL, --olabel=OLABEL
                        new label (erased/replaced old label)
  -o FILE, --otex=FILE  ouput gyri texture with new regions

AimsMesh


    AimsMesh
    --------

Extracts triangulation in a label short volume

Options :

-i | --input | -input <string>
    input short volume label (level 0 is assumed to be the background)

[ -o | --output | -output <string> ]
    output mesh prefix name (extension will determine the format)
    [default=filein]

[ -l | --label | -label <S32> ]
    labelInf: extracts only label in [<labelInf>;<labelSup>]

[ -L | --Label | -Label <S32> ]
    labelSup: extracts only label in [<labelInf>;<labelSup>]

[ -S | --Surface | -Surface <FLOAT> ]
    minimum surface of the interfaces to extract [default=0.0 mm^2]

[ --smooth <boolean> ]
    smoothes the mesh [default=no smoothing]

[ --smoothType <string> ]
    smoothing alorithm's type : laplacian, simplespring, polygonspring or
    lowpass [default=lowpass]

[ --smoothIt <S32> ]
    smoothing number of iterations [default=30]

[ --smoothRate <FLOAT> ]
    smoothing moving rate at each iteration [default=0.4]

[ --smoothAngle <FLOAT> ]
    smoothing feature angle (in degrees) below which the vertex is not moved,
    only for the Laplacian algorithm, between 0 and 180 degree [default=0]

[ --smoothForce <FLOAT> ]
    smoothing restoring force for the Simple Spring and Polygon Spring
    algorithm, between 0 and 1 [default=0.2]

[ --decimation <boolean> ]
    decimate the mesh [default=no decimation]

[ --deciReductionRate <FLOAT> ]
    expected % decimation reduction rate [default=99%]

[ --deciMaxClearance <FLOAT> ]
    maximum clearance of the decimation [default=3.0]

[ --deciMaxError <FLOAT> ]
    maximum error distance from the original mesh (mm)  [default=1.0]

[ --deciAngle <FLOAT> ]
    feature angle (degrees), between 0 and 180 [default=180]

[ --split <boolean> ]
    split the surface corresponding to one connected component into
    sub-surfaces, each corresponding to an interface between 2 different
    components [default=no splitting]

[ --minFacetNumber <S32> ]
    minimum number of facets to allow decimation [default=50]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMesh2Ascii

usage : bin/AimsMesh2Ascii filein.mesh fileout.txt

AimsMesh2SSGraph

bin/AimsMesh2SSGraph [-p prim.arg] [-s surftype] [-b] [-t trans] [-g growmode] in.mesh inflate.mesh outgraph.arg irm.ima textures...
Makes a primal sketch graph from a mesh and a set of smoothed textures

Options :
-p    prim.arg : make also the corresponding primal sketch graph
-s    surftype : tore (default) or surface
-b             : blobs are already extracted, don't search for them
                 (textures are labels)
-t    trans    : initial translation of extracted surfaces (default: 0)
-g    growmode : mesh growing mode along scales: scale (default), translate, or pushnormal

AimsMesh2Sphere


    AimsMesh2Sphere
    ---------------

Build a spherical coordinate system on a mesh

Options :

-i <file name (read only): Mesh of VOID>
    input mesh

-o <filename: Mesh of VOID>
    result

[ -t <filename: texture of POINT2DF> ]
    output 2D coord texture

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshArea


    AimsMeshArea
    ------------

Prints a mesh surface area

Options :

-i | --input <file name (read only): Mesh of VOID>
    input mesh

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshAverage


    AimsMeshAverage
    ---------------

Average a time series mesh.
WARNING: Be sure that the nodes at different time serie correspond to the same
point...

Options :

-m | --mesh <string>
    input time series mesh

-o | --output <string>
    output mean mesh

[ -v | --variability <string> ]
    variability output texture

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshBlobExtract


    AimsMeshBlobExtract
    -------------------

Extract blobs

Options :

-i | --input <string>
    input mesh file

-t | --texture <string>
    object definition

-o | --output <string>
    output texture file (blobs)

[ -T | --Time | --time <S32> ]
    time point [default = 0]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshBrain


    AimsMeshBrain
    -------------

Computes the brain surface from a segmented image and saves it in a triangles
mesh format file

Options :

-i | --input | -input <string>
    input volume label (short int data), level 0 is assumed to be the back

[ -o | --output | -output <string> ]
    output file name for the mesh [default: same basename as input]

[ --smoothType <string> ]
    smoothing alorithm's type : laplacian, simplespring, polygonspring or
    lowpass [default=lowpass]

[ --smoothIt <S32> ]
    smoothing number of iterations [default=30]

[ --smoothRate <FLOAT> ]
    smoothing moving rate at each iteration [default=0.4]

[ --deciMaxClearance <FLOAT> ]
    maximum clearance expected in the resulting mesh, in mm [default= 1.8]

[ --deciMaxError <FLOAT> ]
    maximum error distance from the original data, in mm [default = 1.0]

[ --minFacetNumber <U32> ]
    minimum number of facets to allow decimation [default=50]

[ --internalinterface <boolean> ]
    mesh the internal interface of the main object [default=false]

[ --ascii <boolean> ]
    write file in ASCII mode if the format supports it [default=binary]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshCC2Arg


    AimsMeshCC2Arg
    --------------

Converts a Connected Component texture into a graph

Options :

-i | --input <string>
    input mesh file

-o | --output <string>
    output graph (*.arg) file

-t | --texture <string>
    CC definition

-v | --volume <string>
    volume for voxel sizes and dimensions

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshCheckClosed


    AimsMeshCheckClosed
    -------------------

Check if a mesh is closed. The program exists with failure state if the input
mesh is not closed.

Options :

-i | --input <file name (read only): Mesh of VOID>
    input mesh

[ -o | --output <string> ]
    output bad vertices file

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshConnectedComponent


    AimsMeshConnectedComponent
    --------------------------

Connected Components in a label texture

Options :

-i | --input <string>
    input mesh file

-t | --texture <string>
    object definition texture

-o | --output <string>
    output connected components texture file

[ -T | --Threshold <FLOAT> ]
    threshold applied to binarize the input texture [0]

[ -m <S32> ]
    mode: 1: lesser than threshold, 0: greater [default=0]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshCurvature


    AimsMeshCurvature
    -----------------

Estime the mean curvature of a mesh

Options :

-i | --input <string>
    input file

-o | --output <string>
    output texture

-m | --method <string>
    method: "fem" -> finite elements, "boix" -> Boix, "barycenter" ->
    barycenter, "boixgaussian" -> Boix Gaussian

[ -r | --ratio <FLOAT> ]
    proportion (%) of point to be thresholded 

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshCut


    AimsMeshCut
    -----------

Cuts a mesh by a plane

Options :

-i | --input <file name (read only): Mesh of VOID>
    input mesh

-o | --output <filename: Mesh of VOID>
    output cutout mesh

-a <FLOAT>
    plane equation coef: a

-b <FLOAT>
    plane equation coef: b

-c <FLOAT>
    plane equation coef: c

-d <FLOAT>
    plane equation coef: d

[ -p | --plane <filename: Mesh of VOID> ]
    output plane intersection mesh

[ --border <filename: Segments of VOID> ]
    output border polygon

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshDecimation


    AimsMeshDecimation
    ------------------

Decimates a triangulation

Options :

-i | --input <file name (read only): Mesh of VOID>
    input triangulation

[ -o | --output <filename: Mesh of VOID> ]
    output triangulation

[ --smooth <S32> ]
    smoothes the mesh [default is no smoothing]

[ --smoothType <string> ]
    smoothing alorithm's type : laplacian, simplespring, polygonspring or
    lowpass [default=lowpass]

[ --smoothIt <S32> ]
    smoothing number of iterations [default=30]

[ --smoothRate <FLOAT> ]
    smoothing moving rate at each iteration [default=0.4]

[ --smoothAngle <FLOAT> ]
    smoothing feature angle (in degrees) below which the vertex is not moved,
    only for the Laplacian algorithm, between 0 and 180 degree [default=0]

[ --smoothForce <FLOAT> ]
    smoothing restoring force for the Simple Spring and Polygon Spring
    algorithm, between 0 and 1 [default=0.2]

[ --deciReductionRate <FLOAT> ]
    decimation reduction rate expected in % [default=99%]

[ --deciMaxClearance <FLOAT> ]
    maximum clearance of the decimated mesh expected in mm [default=10]

[ --deciMaxError <FLOAT> ]
    maximum error distance from the original mesh in mm [default=10]

[ --deciAngle <FLOAT> ]
    feature angle in degrees, between 0 and 180: angle formed by local mesh
    edges above which edges are preferably not smoothed [default=180: no
    filtering]

[ --ascii <S32> ]
    write *.mesh in ASCII [default=binar]

[ --precisionmap <file name (read only): texture of FLOAT> ]
    precision map texture: if provided, use this texture to determine if
    vertices can be removed easily or not during decimation, instead of the
    default edges angles (see --deciAngle parameter)

[ --precthreshold <vector of FLOAT> ]
    precision map thresholds (see --precisionmap parameter): vertices with
    precision above the threshold are not removed at a given iteration step.
    Several values may be used for the successive iteration steps.
    If no threshold is provided, the proportion from the decimation reduction
    rate is used at step 0, then increases exponentially to asymtotically reach
    the max precision within about 20 steps

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshDistance


    AimsMeshDistance
    ----------------

Compute geodesic distance to object

Options :

-i | --input <string>
    input mesh file

-o | --output <string>
    output distance texture file

-t | --texture <string>
    object definition texture

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshGenerate


    AimsMeshGenerate
    ----------------

Generates a common-shaped mesh

Options :

-i | --input <string>
    input parameter file (.minf-like)
    Possible types and parameters:
    
    type : arrow
    arrow_length_factor : relative length of the head
    arrow_radius : radius of the tail
    facets : (optional) number of facets of the cone section (default: 4)
    point1 : 3D position of the head
    point2 : 3D position of the center of the bottom
    radius : radius of the head
    
    type : cone
    closed : (optional) if non-zero, make polygons for the cone end (default:
    0)
    facets : (optional) number of facets of the cone section (default: 4)
    point1 : 3D position of the sharp end
    point2 : 3D position of the center of the other end
    radius : radius of the 2nd end
    smooth : (optional) make smooth normals and shared vertices (default: 0)
    
    type : cube
    center : 3D position of the center
    radius : half-length of the edge
    smooth : (optional) make smooth normals and shared vertices (default: 0)
    
    type : cylinder
    closed : (optional) if non-zero, make polygons for the cylinder ends
    (default: 0)
    facets : (optional) number of facets of the cylinder section (default: 4)
    point1 : 3D position of the center of the 1st end
    point2 : 3D position of the center of the 2nd end
    radius : radius of the 1st end
    radius2 : (optional) radius of the 2nd end (default: same as radius)
    smooth : (optional) make smooth normals and shared vertices (default: 0)
    
    type : ellipse
    center : 3D position of the center, may also be specified as 'point1'
    parameter
    facets : (optional) number of facets of the sphere. May also be specified
    as 'nfacets' parameter (default: 225)
    radius1 : radius1
    radius2 : radius2
    uniquevertices : (optional) if set to 1, the pole vertices are not
    duplicated( default: 0)
    
    type : icosahedron
    center : 3D position of the center
    radius : radius
    
    type : icosphere
    center : 3D position of the center, may also be specified as 'point1'
    parameter
    facets : (optional) minimum number of facets of the sphere. (default: 30)
    radius : radius
    
    type : sphere
    center : 3D position of the center, may also be specified as 'point1'
    parameter
    facets : (optional) number of facets of the sphere. May also be specified
    as 'nfacets' parameter (default: 225)
    radius : radius
    uniquevertices : (optional) if set to 1, the pole vertices are not
    duplicated( default: 0)
    
    type : circle
    center : 3D position of the center
    normal : (optional) normal vector to the circle plane (default: (0, 0, 1))
    radius : radius of the circle
    segments : (optional) number of segments in the circle polygon (default:
    20)
    start_angle : (optional) start angle for incomplete circle (default: 0)
    start_direction : (optional) vector in the circle plane determining the
    beginning of angles (circle ray) (default: (1, 0, 0))
    stop_angle : (default) stop angle for incomplete circle (default: 2*pi)
    
    type : grid
    boundingbox_max : 3D position of the higher bounding box
    boundingbox_min : 3D position of the lower bounding box
    grid_sampling : 3D sampling interval
    
    type : parallelepiped
    boundingbox_max : 3D position of the higher bounding box
    boundingbox_min : 3D position of the lower bounding box

-o | --output <filename: Mesh of VOID>
    output mesh

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshGeodesicDepth


    AimsMeshGeodesicDepth
    ---------------------

Compute geodesic depth on a triangulation

Options :

-i | --input <string>
    input mesh file

-o | --output <string>
    output depth texture file

-v | --volume <string>
    brain hull definition (binary image relative to the triangualtion)

[ -c | --close <FLOAT> ]
    radius of the closing [default = 10]

[ -e | --erosion <FLOAT> ]
    radius of the erosion [default = 5]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshLineMeasurement


    AimsMeshLineMeasurement
    -----------------------

Measurement along a line on a mesh

Options :

-i | --input <file name (read only): Mesh of VOID>
    input mesh

-p1 <POINT3DF>
    3D position of the starting point (x,y,z)

-p2 <POINT3DF>
    3D position of the end point (x,y,z)

[ -o | --output <filename: texture of FLOAT> ]
    output texture line (default: not written)

[ -m <string> ]
    mode: 'shortest' line, 'plane' line (default: shortest)

[ -pe <VECTOR_OF_4_FLOAT> ]
    plane equation for 'plane' mode (see -m option) (a,b,c,d) for plane
    ax+by+cz+d=0

[ -r <FLOAT> ]
    ratio of the length between p1 and p2 where a point has to be determined
    (default: 1)

[ -pe2 <VECTOR_OF_4_FLOAT> ]
    half-space (plane equation) where to look for the target point in case of
    ambiguity (useful only in 'plane' mode) (default: no restriction)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshParcellation2VolumeParcellation


    AimsMeshParcellation2VolumeParcellation
    ---------------------------------------

Project a mesh parcellation to a volume

Options :

-t | -texture <file name (read only): texture of S16>
    input label (short) texture

-m | -mesh <file name (read only): Mesh of VOID>
    input mesh

-o | -output <string>
    output parcellation volume

-v | -volume <string>
    input volume file

[ -l | -label <S16> ]
    label of the object in the volume (default = 100)

[ -T | -Time | -time <U32> ]
    make graph from time T of input texture

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshSmoothing


    AimsMeshSmoothing
    -----------------

Smoothes a triangulation

Options :

-i | --input <file name (read only): Mesh of VOID>
    input triangulation

[ -o | --output <filename: Mesh of VOID> ]
    output triangulation

[ --algoType <string> ]
    alorithm's type : laplacian, simplespring, polygonspring or lowpass
    [default=lowpass]

[ --nIteration <S32> ]
    number of iterations [default=30]

[ --rate <FLOAT> ]
    moving rate at each iteration [default=0.4]

[ --featureAngle <FLOAT> ]
    feature angle (in degrees) below which the vertex is not moved, only for
    the Laplacian algorithm, between 0 and 180 degree [default=0]

[ --springForce <FLOAT> ]
    restoring force for the Simple Spring and Polygon Spring algorithm, between
    0 and 1 [default=0.2]

[ --ascii <S32> ]
    write *.mesh in ASCII [default=binar]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshTransform


    AimsMeshTransform
    -----------------

Applies a transformation to a mesh

Options :

-i | --input <file name (read only): Mesh of VOID>
    input mesh

[ -o | --output <filename: Mesh of VOID> ]
    output (transformed) mesh [default: same as input]

[ -t | --transform <string> ]
    transformation file *.trm

[ -a | --ascii <boolean> ]
    write in ascii format

[ --scaleX <FLOAT> ]
    specify X scale factor

[ --scaleY <FLOAT> ]
    specify Y scale factor

[ --scaleZ <FLOAT> ]
    specify Z scale factor

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshWatershed.py

usage: AimsMeshWatershed.py [-h] [--basins_size BASINS_SIZE]
                            [--basins_depth BASINS_DEPTH] [--mode MODE]
                            [--threshold THRESHOLD]
                            normedprofile whitemesh basins

-------------------------------------------------------------------
Compute  the ROIs from the watershed algorithm.
Select the ROIs according to two main criteria: their size and
their depth.
Generate a reduced profile by basins.
-------------------------------------------------------------------

positional arguments:
  normedprofile         input normed connectivity profile
  whitemesh             input white mesh
  basins                output basins segmentation

optional arguments:
  -h, --help            show this help message and exit
  --basins_size BASINS_SIZE
                        size criteria to regroup smallest parcels
  --basins_depth BASINS_DEPTH
                        depth criteria to regroup parcels
  --mode MODE           mode of merging : mode = 'and': merge done if
                        parcel_size < k_size and parcel_depth < k_depth mode =
                        'or' idem with or operator : more merges
  --threshold THRESHOLD
                        threshold on the input texture intensities

AimsMeshWhite


    AimsMeshWhite
    -------------

Computes the brain surface from a segmented image as a mesh

Options :

-i | --input <string>
    input short volume label (level 0 is assumed to be the background)

[ -o | --output <string> ]
    output mesh filename [default=input + mesh extension]

[ --deciMaxClearance <FLOAT> ]
    maximum clearance expected in the resulting mesh in the decimation process,
    in mm [default= 5 mm]

[ --deciMaxError <FLOAT> ]
    maximum expected error distance from the original data in the decimation
    process, in mm [default = 3 mm]

[ --minFacetNumber <S32> ]
    minimum number of facets to allow decimation [default=50]

[ --ascii <boolean> ]
    write mesh file in ASCII mode if supported by the format [default=binary]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshes2Graph


    AimsMeshes2Graph
    ----------------

Makes a graph from a set of meshes

Options :

-o | -output <string>
    output data graph

[ -n | --name <string> ]
    name attribute given to the graph's nodes (default=name of corresponding
    mesh file)

[ -i | -input <vector of string> ]
    input meshes filenames

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMoment


    AimsMoment
    ----------

Compute the invariant moments

Options :

-i | --input <string>
    input volume (in 8 or 16 bits) or triangulated mesh

[ -l | --label <S32> ]
    object label in raster image [default=all label]

[ -o | --output <string> ]
    ASCII result file name [default=stdout]

[ -m | --mode <string> ]
    mode: f -> full, i -> invariant only [default=f]

[ -t | --type <string> ]
    type: v -> volumic, s -> surfacic [default=v] (only for triangulated mesh)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMorphoMath


    AimsMorphoMath
    --------------

Morphological operators (erosion, dilation, closing, opening)
for both binary and gray level intensity images

Options :

[ -i <file name (read only): { Volume of DOUBLE, Volume of FLOAT, Volume of S16,
    Volume of S32, Volume of S8, Volume of U16, Volume of U32, Volume of U8 }>
    Input image ]

[ -r <FLOAT> ]
    Radius parameter (in mm)

[ -m <string> ]
    Mode that can be:
    
    ero --> erosion
    dil --> dilation
    clo --> closing
    ope --> opening

[ -o <string> ]
    Output image

[ -c <boolean> ]
    do not use chamfer binary mathematical morphology (default: use it when
    available)

[ -x <S32> ]
    X size of the chamfer distance mask (unused with grey level morpho)
    [default=3]

[ -y <S32> ]
    Y size of the chamfer distance mask (unused with grey level morpho)
    [default=3]

[ -z <S32> ]
    Z size of the chamfer distance mask (unused with grey level morpho)
    [default=3]

[ -f <FLOAT> ]
    chamfer multiplication factor (unused with grey level morpho) [default=50]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsNormDiff


----------------------------------------------------------------
AimsNormDiff                                                    
            -r[eference image]   < ref filename >               
            -c[ompared image]    < compared filename >          
            -a[ref to mri dep]   <filename >                    
            -b[com to mri dep]   <filename >                    
            -o[utput]            < norm image >                 
           [-h[elp]]                                            
----------------------------------------------------------------
 Compute ration (R - C) / R                                     
----------------------------------------------------------------

AimsNormWithRegion


----------------------------------------------------------------
AimsNormWithRegion                                              
            -i[nput series]   < dynamic series >                
            -v[oi]      < voifile >                             
            -m[otion]    < motionfile (default is identity) >    
            -n[ame]     < reference ROI name (from selectionlist)>
            -o[utput]   < norm image >                          
            -s[elector] < user defined selector file name >     
            -l[ist]     < list of available template selectors> 
            -d[ose]     < injected dose > 
            --hierarchy < hierarchyfile >                       
            --selection < template selector>                    
           [-h[elp]]                                            
----------------------------------------------------------------
     dyn series   : input dynamic data                           
     motionfile   : displacement file default val : Identity     
     voifile      : file containing roi information see(--voitype)
     injected dose: if injected dose is specified, ROI          
                    activity is normalized by this dose :       
                    (Region - Reference)/Dose.                  
                    Otherwise it is normalized by the reference 
                    ROI name : (Region - Reference)/Reference   
                                                                
       --selection:   template selector name  available         
                 :        selectors may be listed (switch -l)   
                 :    OR                                        
                 :    all to disable selection mode             
                                                                
----------------------------------------------------------------

AimsOpening

-----------------------------------------------------------------------
AimsOpening has been replaced by AimsMorphoMath. Please use it instead.
-----------------------------------------------------------------------

AimsOverVolume


    AimsOverVolume
    --------------

Change the dimension of an image

Options :

-i | --input <string>
    source volume

-o | --output <string>
    destination volume

--dx <S32>
    size of the output volume

--dy <S32>
    size of the output volume

--dz <S32>
    size of the output volume

--dt <S32>
    size of the output volume

[ --x0 <S32> ]
    translation (int) of the input image (default = none)

[ --y0 <S32> ]
    translation (int) of the input image (default = none)

[ --z0 <S32> ]
    translation (int) of the input image (default = none)

[ --t0 <S32> ]
    translation (int) of the input image (default = none)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsPCAfilter


    AimsPCAfilter
    -------------

PCAnalysis 

Options :

-i <file name (read only): volume of FLOAT>
    input file

[ -c <S32> ]
    for mask closing (default 1)

[ -r <S32> ]
    for reduction (default 0)

[ -n <S32> ]
    for temporal normalisation (default 0, 1-->max, 2-->euclid)

[ --am <S32> ]
    for  median aggreg (default 0)

[ --fm <S32> ]
    for median filt  (default 0)

[ --rx <S32> ]
    x resolution (default 1)

[ --ry <S32> ]
    y resolution (default 1)

[ --rz <S32> ]
    z resolution (default 1)

[ --vp <S32> ]
    eigenvalues kept (default 6)

[ -verbose <boolean> ]
    yields some more info

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsPCAloc


    AimsPCAloc
    ----------

LocalPCAnalysis 

Options :

-i <file name (read only): volume of FLOAT>
    input files 

[ -verbose <boolean> ]
    yields some more info

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsPCAloc2


    AimsPCAloc2
    -----------

PCAnalysis 

Options :

-i <file name (read only): volume of FLOAT>
    input files 

[ -verbose <boolean> ]
    yields some more info

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsParamCorrectDti


-------------------------------------------------------------------------
AimsParamCorrectDTI -d[istorded] <distorded>                             
                    -o[utput] <fileout>                                  
                    -p[arameter] <param>                                 
                   [--memMap]                                            
                   [-r[ead] <reader>]                                    
                   [-h[elp]]                                             
-------------------------------------------------------------------------
Correction of DTI distorsions from an existing parameter file            
-------------------------------------------------------------------------
     distorded    : source S16 distorded data                            
     fileout      : destination S16 data file name                       
     param        : parameter file containing corrections                
     memMap       : memory mapping activated (obsolete, automatic)       
-------------------------------------------------------------------------

AimsParameterize2DImageDomain


    AimsParameterize2DImageDomain
    -----------------------------

Lissage couplé d'un couple d'images 2D avec des contraintes 

Options :

[ -i1 | --input1 <string> ]
    input Image1

[ -i2 | --input2 <string> ]
    input Image2

-c1 | --cont1 <string>
    input constraint1

-c2 | --cont2 <string>
    input constraint2

-o1 | --output1 <string>
    output Image1

-o2 | --output2 <string>
    output Image2

-t | --scale <FLOAT>
    scale

[ -dt | --deltat <FLOAT> ]
    time step (diffusion only; default=0.1)

[ -a <FLOAT> ]
    diffusion weight

[ -b <FLOAT> ]
    constraints term

[ -g <FLOAT> ]
    coupling term

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsPowerComb


------------------------------------------------------------------
AimsPowerComb  -i <i1>  [-a <num1>] [-b <den1>]                  
               [-j <i2>  [-c <num2>] [-d <den2>]]                 
               [-e <cst>]                                         
                -o[utput] <fileout>                               
               [-t[ype] <datatype>                                
               [-h[elp]]                                          
------------------------------------------------------------------
Power combination e * I1^(a/b) * I2^(c/d)                         
                                                                  
Note : a,b,c,d,e must be real                                     
------------------------------------------------------------------
     i1      : first data (volume or texture)                     
     num1    : multiplicative coefficient for the first data [1.0]
     den1    : divisor coefficient for the first data [1.0]       
     i2      : second data (volume or texture)                    
               (if none, I1^(a/b) ) 
     num2    : multiplicative coefficient for the second data[1.0]
     den2    : divisor coefficient for the second data [1.0]      
     cst     : constant offset value [default=1.0]                
     fileout : destination data                                   
     datatype: data type of the destination volume/texture (S16, U8, ...) 
               [default=type of in1]                              
               For texture, i1, i2 and fileout must have the same type
------------------------------------------------------------------

AimsRFdf


    AimsRFdf
    --------

 Lit des donnees Fdf

Options :

-i <string>
    input data filename

[ -o <string> ]
    output label data filename

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsRTiff


    AimsRTiff
    ---------

 Lit des données Tiff

Options :

-i <string>
    input data filename

[ -o <string> ]
    output label data filename

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsRefineMesh


    AimsRefineMesh
    --------------

Mesh refinement

Options :

-i <file name (read only): Mesh of VOID>
    input mesh

-o <filename: Mesh of VOID>
    output mesh

[ -a <boolean> ]
    write in ascii format

-l <FLOAT>
    maximum edge length in mm

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsRegisterBMEstimate


    AimsRegisterBMEstimate
    ----------------------

Compute registrations between two 2D or 3D volumes

Options :

-r <string>
    Input reference data

-t <string>
    Input test data

[ -o <string> ]
    Output data

[ -bv <string> ]
    Background value to use

[ -cr <S32> ]
    Channel of multi-channel reference image to use during registration
    estimation
    Possible types and values:
    type : RGB or RGBA
    values: 0=red, 1=green, 2=blue, 3=alpha, 4=norm
    
    type : HSV
    values: 0=hue, 1=saturation, 2=value, 4=norm
    
    [default is set to norm]
    

[ -ct <S32> ]
    Channel of multi-channel test image to use during registration estimation
    Possible types and values:
    type : RGB or RGBA
    values: 0=red, 1=green, 2=blue, 3=alpha, 4=norm
    
    type : HSV
    values: 0=hue, 1=saturation, 2=value, 4=norm
    
    [default is set to same value as reference channel]
    

[ -m <string> ]
    Initialisation motion (default = identity)

[ -n <string> ]
    Output motion (default = <test data directory>/<test>_TO_<ref>.trm)

[ --inv <boolean> ]
    Inverse output motion, if 1 default output motion name will be = <test data
    directory>/<ref>_TO_<test>.trm (default = 0)

[ --start <S32> ]
    Starting pyramid level (default = auto)

[ --stop <S32> ]
    End pyramid level (default = auto)

[ --transfo <S32> ]
    Transformation type : 1 for rigid, 2 for similitude, 3 for affine (default
    = 1)

[ --Xsize <S16> ]
    X size of the bloc in voxel (default = 4)

[ --Ysize <S16> ]
    Y size of the bloc in voxel (default = 4)

[ --Zsize <S16> ]
    Z size of the bloc in voxel (default = 4)

[ --cutVar <DOUBLE> ]
    % initial de blocs de plus forte variance conserves (default=auto)

[ --stopVar <DOUBLE> ]
    Minimum du % de blocs conserves (default=auto)

[ --%kept <DOUBLE> ]
    % de blocs de plus faibles residus conserves pour l'estimation robuste
    (default=0.5)

[ --correlThresh <DOUBLE> ]
    Threshold on the similarity criterion norm (default=-1, no threshold)

[ --lthRef <DOUBLE> ]
    Low grey level threshold on ref image (default = -100000)

[ --hthRef <DOUBLE> ]
    High grey level threshold on ref image (default = +100000)

[ --lthTest <DOUBLE> ]
    Low grey level threshold on test image (default = -100000)

[ --hthTest <DOUBLE> ]
    High grey level threshold on test image (default = +100000)

[ --iter <S32> ]
    Maximum number of iterations per pyramid level (default=3)

[ --field <string> ]
    Displacement field

[ --Info <string> ]
    List all the initial parameters : y or n (default=y)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsRegisterFFDApply


    AimsRegisterFFDApply
    --------------------

Apply FFD (vector field) transformation on an image, a mesh, a 'bucket' (voxels
list file), fiber tracts, a graph, or to points.

Note that on images the vector field normally represents the inverse
transformation (for a destination point we seek the source position of the
point), but for meshes, buckets, fibers, or points the vector field is applied
directly (a vertex is moved according to the vector field), so the
transformation should be the inverse of the one applied to an image. Similarly,
any affine transform given as -m option is from the source object to the input
deformation space.

In points mode, the -i options either specifies an ASCII file containing point
coordinates, or is directly one or several points coordinates. Points shoud be
in the shape (x, y, z) with parentheses.

Note also that for meshes or points, the dimensions, voxel sizes, grid,
reference, and resampling options are pointless and are unused. Only the vector
field interpolation (--vi) option is used.

In Buckets and graph mode, the options --sx, --sy, --sz allow to specify the
output voxel size, but the reference (-r) is not used so far. The
transformation field is applied independently on each bucket voxel with no
resampling, so objects may end up with holes.

Options :

-i | --input <file name (read only): { Bucket of VOID, BundleMap of VOID, Graph
    of VOID, Mesh of VOID, Mesh2 of VOID, Mesh4 of VOID, Volume of DOUBLE,
    Volume of FLOAT, Volume of POINT3DF, Volume of RGB, Volume of RGBA, Volume
    of S16, Volume of S32, Volume of S8, Volume of U16, Volume of U32, Volume
    of U8 }>  Input image

[ -d <string> ]
    Input control knots grid

[ -m | --motion <string> ]
    Input affine transformation [Test_TO_Ref.trm]

[ -t | --type <string> ]
    Voxel values resampling type : n[earest], l[inear], c[ubic] [default =
    cubic]

[ -bv <string> ]
    Background value to use

[ --dx <S32> ]
    Output X dimension [default: same as input]

[ --dy <S32> ]
    Output Y dimension [default: same as input]

[ --dz <S32> ]
    Output Z dimension [default: same as input]

[ --sx <DOUBLE> ]
    Output X voxel size [default: same as input]

[ --sy <DOUBLE> ]
    Output Y voxel size [default: same as input]

[ --sz <DOUBLE> ]
    Output Z voxel size [default: same as input]

[ -r | --reference <string> ]
    Volume used to define output voxel size and volume dimension (values are
    overrided by --dx, --dy, --dz, --sx, --sy and --sz)

-o | --output <string>
    Output image

[ -b | --bucket <string> ]
    Output bucket knots

[ -g | --grid <string> ]
    Output grid mesh

[ -c | --compression <string> ]
    Output compression volume

[ --old-mode <boolean> ]
    Make this command work with pre-2015 FFD motions (which are in voxels
    instead of millimetres) [default: false]

[ --vi | --vectorinterpolation <string> ]
    Vector field interpolation type: l[inear], c[ubic] [default = cubic]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsRegisterFFDEstimate


    AimsRegisterFFDEstimate
    -----------------------

Estimation of FFD deformation

Options :

-r <string>
    Input reference image

-t <string>
    Input test image

[ -cr <S32> ]
    Channel of multi-channel reference image to use during registration
    estimation
    Possible types and values:
    type : RGB or RGBA
    values: 0=red, 1=green, 2=blue, 3=alpha, 4=norm
    
    type : HSV
    values: 0=hue, 1=saturation, 2=value, 4=norm
    
    [default is set to norm]
    

[ -ct <S32> ]
    Channel of multi-channel test image to use during registration estimation
    Possible types and values:
    type : RGB or RGBA
    values: 0=red, 1=green, 2=blue, 3=alpha, 4=norm
    
    type : HSV
    values: 0=hue, 1=saturation, 2=value, 4=norm
    
    [default is set to same value as reference channel]
    

-o <string>
    Output FFD field

[ -l <string> ]
    List of VOID bucket

[ -d <string> ]
    Deprecated parameter. Please use -m option using inversed motion
    <test_TO_ref>.

[ -m <string> ]
    Rigid initial displacement <test_TO_ref>

[ -initFFD <string> ]
    Initial FFD field <ctrlshift.ima>

[ -initDEP <string> ]
    Initial Displacement field <Ex: derived from BlockMatching>

[ -icx <S32> ]
    Initial number of control knots / X

[ -icy <S32> ]
    Initial number of control knots / Y

[ -icz <S32> ]
    Initial number of control knots / Z

[ -fcx <S32> ]
    Final number of control knots / X

[ -fcy <S32> ]
    Final number of control knots / Y

[ -fcz <S32> ]
    Final number of control knots / Z

[ -ix <S16> ]
    Increment number of control knots / X

[ -iy <S16> ]
    Increment number of control knots / Y

[ -iz <S16> ]
    Increment number of control knots / Z

[ -dx <FLOAT> ]
    Maximum local deformation (mm) / X

[ -dy <FLOAT> ]
    Maximum local deformation (mm) / Y

[ -dz <FLOAT> ]
    Maximum local deformation (mm) / Z

[ -sfirst <S32> ]
    Nb of iterations before first gain computation (min 1) [default=3]

[ -sfin <FLOAT> ]
    Gain threshold (for the final pyramid level) [default=0.01]>

[ -scoef <FLOAT> ]
    Reduction of the gain threshold / pyramid level [default=1=const]

[ -bref <S32> ]
    Number of bins to use for ref histogram [default=64]>

[ -btest <S32> ]
    Number of bins to use for test histogram [default=64]>

[ -pre <boolean> ]
    Preprocess volumes (flatten masks, 99% cutoff [default=true]

[ -dbgPath <string> ]
    [debug] Directory to write intermediate files [default=/tmp/]

[ -dbgWriteAll <boolean> ]
    [debug] Write all intermediate files [default=false]

[ -dbgWriteJPDF <boolean> ]
    [debug] Write joint histograms [default=false]

[ -dbgWriteParam <boolean> ]
    [debug] Write parameters (i.e. FFD control knots) [default=false]

[ -dbgWriteDerParam <boolean> ]
    [debug] Write parameter derivatives [default=false]

[ -dbgWriteDef <boolean> ]
    [debug] Write deformations [default=false]

[ -dbgWriteContrib <boolean> ]
    [debug] Write joint histogram's contributing points [default=false]

[ -dbgWriteMI <boolean> ]
    [debug] Write the successive mutual information scores [default=false]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsRegisterFFDFromCoordImages


    AimsRegisterFFDFromCoordImages
    ------------------------------

Compute a displacement field (FFD) from transformed coordinate images.

Usage:
1. Create images of X, Y, and Z coordinate with:
python2 -m soma.aimsalgo.scripts.create_coordinate_images
2. Warp these images using whatever tool
3. Feed the warped images back into this program to reconstruct the FFD
displacement field that performs the same warping.
4. You can now use AimsRegisterFFDApply to perform the warping.

Options :

--input-x | -x <file name (read only): VolumeRef of FLOAT>
    transformed image of X coordinates

--input-y | -y <file name (read only): VolumeRef of FLOAT>
    transformed image of Y coordinates

--input-z | -z <file name (read only): VolumeRef of FLOAT>
    transformed image of Z coordinates

--output | -o <filename: VolumeRef of POINT3DF>
    output displacement field

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose | -v [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsRemoveNaN


    AimsRemoveNaN
    -------------

Remove NaN (Not a Number)  values from an image

Options :

-i <file name (read only): { Volume of DOUBLE, Volume of FLOAT }>  input file

[ -o <string> ]
    output file (if ommited, only information about NaN will be showed)

[ --value <DOUBLE> ]
    value used to replace NaN value (default = 0, with default -np value it
    corresponds to the image minimum)

[ -np <boolean> ]
    By default value is expressed in percentage of voxel value: value =
    min+(max-min)*(percentage/100). If this option is used, value is used
    direclty

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsReplaceLevel


    AimsReplaceLevel
    ----------------

Replace gray levels by others

Options :

-i | --input <string>
    input

-o | --output <string>
    outpout

-g | --graylevel <vector of string>
    gray levels or RGB/RGBA values to replace

-n | --new <vector of string>
    new values for gray levels or RGB/RGBA

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsResample


    AimsResample
    ------------

Resampling. Applies a transformation matrix to a volume. Performs linear
resampling by default.

Options :

-i | --input <file name (read only): { Volume of DOUBLE, Volume of FLOAT,
    Volume of RGB, Volume of RGBA, Volume of S16, Volume of S32, Volume of S8,
    Volume of U16, Volume of U32, Volume of U8 }>  source volume

-o | --output <string>
    destination volume

[ -m | --motion <string> ]
    motion file [default=identity]

[ --dx <S32> ]
    dimx of the resampled volume

[ --dy <S32> ]
    dimy of the resampled volume

[ --dz <S32> ]
    dimz of the resampled volume

[ --sx <FLOAT> ]
    voxel x dimension of the resampled volume

[ --sy <FLOAT> ]
    voxel y dimension of the resampled volume

[ --sz <FLOAT> ]
    voxel z dimension of the resampled volume

[ -t | --type <string> ]
    Resampling type: n[earest], l[inear], q[uadratic], c[cubic], quartic,
    quintic, six[thorder], seven[thorder] [default=linear]. Modes may also be
    specified as order number: 0=nearest, 1=linear etc.

[ -r | --reference <string> ]
    Volume used to define output voxel size and volume dimension (values are
    overrided by --dx, --dy, --dz, --sx, --sy and --sz)

[ -d | --defaultvalue <string> ]
    Default value for borders [default=0]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsRoiFeatures


    AimsRoiFeatures
    ---------------

Compute simple statistics on one or more images from regions of interest.
Features computed are min, max, mean, standard deviation and median. The images
on which the statistics are done can also be combined with images of weights
(like a probabilistic map), all the statistiques will then be weighted.
The output can be in minf or csv format (see -f option below). In minf format,
its a dictionary containing one sub-dictionary per ROI. Each sub-dictionary
contains one entry per feature (identified by the label of the feature). In csv
format it is a text file containing values separated by tabulation character
and compatible with main spread sheet software such as OpenOffice and Excel.

Examples:

1) To compute the statistics of region drawn in Anatomist on a single image:

	AimsRoiFeature -i regionsDrawnWithAnatomist.arg -s image.ima

2) To compute the statistics of regions defined in an image of labels on
several images:

	AimsRoiFeature -i imageOfLabels.ima -s first_image.ima second_image.ima

3) To compute statistics on several images with the same filename:

	AimsRoiFeature -i imageOfLabels.ima -s first:first/image.ima
second:second/image.ima

4) Same as 3) but save the result in csv format:

	AimsRoiFeature -i imageOfLabels.ima -s first:first/image.ima
second:second/image.ima -f csv

5) Same as 4) but use french locale (i.e. comma for decimal point in numbers):

	AimsRoiFeature -i imageOfLabels.ima -s first:first/image.ima
second:second/image.ima -f csv -l fr

6) To compute statistics on several images combined with weighted images:

	AimsRoiFeature -i imageOfLabels.ima -s first_image.ima second_image.ima -w
first_weight.ima second_weight.ima

	AimsRoiFeature -i imageOfLabels.ima -s first:first/image.ima
second:second/image.ima -w first:weight.ima second:weight.ima


Options :

-i | --input <string>
    Input ROI file (either ROI graph or image).

[ -s | --imageStatistics <vector of string> ]
    Compute statistics from one or more images. Each argument of this parameter
    can be either an image or a graph. The file name can be prefixed with
    <label>: to specify the label that will be used to identify the image in
    the output (by default, the file name without extention is used).

[ -w | --imageWeights <vector of string> ]
    Images of weights, this parameter should have the same structure as
    imageStatistics paramater, same number of arguments and same label (but it
    can be the same image several times).

[ -t | --transformation <file name (read only): AffineTransformation3d> ]
    Transformation between ROI and images (default = identity).

[ --inv <boolean> ]
    Invert transformation. Default direction is ROI to Images. Set this to true
    if your transformation is Images to ROI.

[ -o | --output <string> ]
    Output file name (default = standard output).

[ -f | --format <string> ]
    Output file format. Possible formats are minf or csv. Default value:
    guessed according to file name extension, if the extension is unknown, the
    minf format is used.

[ -l | --locale <string> ]
    Change the locale used for writing numbers in csv format. For instance, to
    use a csv file in a french version of Excel, one should use a french locale
    with "-l fr_FR.utf8".

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSNR


    AimsSNR
    -------

SNR of a VOI in a 3D image

Options :

-i | --input <string>
    3D volume file

[ -v | --voi <string> ]
    U08 mask file of the V.O.I.

[ -x <S16> ]
    X coord of center of a spherical ROI

[ -y <S16> ]
    Y coord of center of a spherical ROI

[ -z <S16> ]
    Z coord of center of a spherical ROI

[ -R <FLOAT> ]
    radius of a spherical ROI

[ -o | --output <string> ]
    output file [default=stdout]

[ --line <boolean> ]
    format of the output file [default=detailed]
    detailed in two columns or just a line a value

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSTAP.py

Usage: Split the STAP part of the superior temporal sulcus (S.T.s.med) in a sulcal graph (Leroy et al, PNAS 2015)

Options:
  -h, --help            show this help message and exit
  -i INPUT, --input=INPUT
                        input labelled sulcal graph
  -o OUTPUT, --output=OUTPUT
                        output labelled sulcal graph
  -l LABEL_ATTR, --label-attr=LABEL_ATTR
                        label attribute, default: guessed grom graph, or label
  --la=LEFT_ANT         left anterior Y limit of the STAP (Talairach coord),
                        default: 12.000000
  --lp=LEFT_POST        left posterior Y limit of the STAP (Talairach coord),
                        default: 45.000000
  --ra=RIGHT_ANT        right anterior Y limit of the STAP (Talairach coord),
                        default: 8.000000
  --rp=RIGHT_POST       right posterior Y limit of the STAP (Talairach coord),
                        default: 42.000000

AimsSegmentsToMesh


--------------------------------------------------------------------------
AimsSegmentsToMesh  -i[nput] <filein>                                     
           -o[utput] <fileout>                                            
         [ -w[idth] ] <size>                                              
         [ -v[erbose] ]                                                   
         [ -h[elp] ]                                                      
--------------------------------------------------------------------------
 Take a list of segments (pairs of points) and build a 3D composed of     
 cylinders. Each cylinder joins two points of a segment.                  
                                                                          
--------------------------------------------------------------------------
-i[nput]            : Serie of pair of 3D points                          
-o[utput]           : Name of the output mesh file                        
-w[idth]            : Width of the cylinder (default 1)                   
-v[erbose]          : display information on standard error output        
-h[elp]             : display the current help message                    
--------------------------------------------------------------------------

AimsSelectLabel


    AimsSelectLabel
    ---------------

Select labels from a label data and put it into a new label data into a new
label data

Options :

-i <string>
    input label data filename

-l <list of S16>
    selected label values

-o <string>
    output label data filename

[ -b <S16> ]
    background label (default=-1)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSetMinf


    AimsSetMinf
    -----------

Set arbitrary tag in the minf file 

Options :

-i | --input <string>
    input data

[ -t | --target <vector of string> ]
    target name

[ -v | --value <vector of string> ]
    value for target

[ -f | --from <string> ]
    from other image

[ -c | --copy <vector of string> ]
    copy given attribute(s) from other image (needs -f option)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSetTransformation.py

Usage: AimsSetTransformation.py [options]

set an affine transformation information in an object header from a
transformation file

Options:
  -h, --help            show this help message and exit
  -i FILE, --input=FILE
                        object to set transformation info on (volume, mesh,
                        etc).
  -t TRMFILE, --transformation=TRMFILE
                        transformation file (*.trm). If not specified and -n
                        option is used, then erase the n-th transformation in
                        list.
  -n TRANSNUM, --number=TRANSNUM
                        set transformation information as the n-th
                        transformation. Default: append at end of list
  -d DESTINATION, --destination=DESTINATION
                        set destination referential name/UUID. Default: try to
                        get it from the transformation file header

AimsSiemensEPI2Volume


----------------------------------------------------------------
AimsSiemensEPI2Volume -i[nput] <filein>                         
                      -o[utput] <fileout>                       
                      -f[irst] <num>                            
                      -s[lices] <nbslice>                       
                      -r[epetitions] <nbrep>                    
                      [-w[rite] <writer>]                       
                      [-h[elp]]                                 
----------------------------------------------------------------
Concatenates all Siemens NEMA EPI images to a 4D data file      
----------------------------------------------------------------
     filein  : origin file                                      
     fileout : output file                                      
     num     : first image number in series                     
     nbslice : number of slices                                 
     nbrep   : number of repetitions                            
----------------------------------------------------------------

AimsSimilarComponentAnalysisSegmentation


    AimsSimilarComponentAnalysisSegmentation
    ----------------------------------------

Similar component analysis automatic segmentation

Options :

-i <string>
    dynamic series file

-o <string>
    fileout segmentation image filename

[ -m <string> ]
    input mask of organism of interest (example: brain mask)

[ -c <S32> ]
    number of classes (default : 12)

[ -r <S32> ]
    number of runs (default : 5)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSlice2Bucket


-------------------------------------------------------------------------
AimsSlice2Bucket -i[nput] <input>                                        
                 -o[utput] <output>                                      
                 -d[ir] <dir>                                            
                [-m[in] <minimum>]                                       
                [-M[ax] <maximum>]                                       
                [-I[ncrement] <inc>]                                     
                [-a[scii]]                                               
                [-h[elp]]                                                
-------------------------------------------------------------------------
 Save slices of a mask to buckets                                        
-------------------------------------------------------------------------
     input         : input S16 or U8 mask data file                      
     output        : output file name for *.bck file                     
     dir           : direction of the slice ('x', 'y' or 'z')            
     minimum       : lower slice index [default=0]                       
     maximum       : upper slice index [default=dim-1]                   
     inc           : increment of slices between two slices [default=1]  
     ascii         : save buckets in ASCII mode [default=binary]         
-------------------------------------------------------------------------

AimsSmoothing


    AimsSmoothing
    -------------

Image filtering
This command allows one to apply a range of filtering algorithms. The user
should choose a filter type, a structuring element (in non-linear cases), and
eventually filter-specific options.

Options :

-i | --input <file name (read only): { Volume of DOUBLE, Volume of FLOAT,
    Volume of RGB, Volume of RGBA, Volume of S16, Volume of S32, Volume of S8,
    Volume of U16, Volume of U32, Volume of U8 }>  source volume

-o | --output <string>
    destination volume

[ -t | --type <string> ]
    Smoothing filter type: mea[n], med[ian], min[imum], max[imum], maj[ority],
    sum, var[iance], sd, gab[or] (default = majority)

[ -s | --strelement <string> ]
    Structuring element type [default:cube]

[ -a | --amplitude <vector of DOUBLE> ]
    Structuring element amplitude [default:1.]

[ -u | --unit <string> ]
    Amplitude unit: v[oxel], m[m] [default:v]

[ --gabSigma <DOUBLE> ]
    Gabor Filter: standard deviation of the gaussian function (mm)
    [default:1.0]

[ --gabTheta <DOUBLE> ]
    Gabor Filter: rotation of the referential (deg) [default:0.0]

[ --gabLambda <DOUBLE> ]
    Gabor Filter: wavelength of the sinusoidal function (mm) [default:1.0]

[ --gabPsi <DOUBLE> ]
    Gabor Filter: phase offset of the sinusoidal function (deg) [default:0.0]

[ --gabGamma <DOUBLE> ]
    Gabor Filter: aspect ratio of the referential [default:1.0]

[ --gabReal <boolean> ]
    Gabor Filter: if true returns the real part, else immaginary [default:true]

[ --bv <string> ]
    Background value to use

[ --dx <S32> ]
    x dimension of the filter to apply (voxels) (deprecated)

[ --dy <S32> ]
    y dimension of the filter to apply (voxels) (deprecated)

[ --dz <S32> ]
    z dimension of the filter to apply (voxels) (deprecated)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSpaghettiModel


----------------------------------------------------------------
AimsSpaghettiModel -i[nput] <filein>                            
                   -o[utput] <fileout>                          
                   [--sx <sx> --sy <sy> --sz <sz>]              
                   [-h[elp]]                                    
----------------------------------------------------------------
creates tensor map with elementary geometrical objects          
----------------------------------------------------------------
     filein  : description file                                 
               +---------------------------------------+        
               | number of objects                     |        
               | dimx dimy dimz                        |        
            -->| CYLINDER                              |        
               | origin  0 5 17                        |        
               | axe     0 1 0                         |        
               | dir     1 1 0                         |        
               | radius  4                             |        
               | length  10                            |        
               | aniso   0.3                           |        
               | lambda1 6.5                           |        
               | deltaL  0.5                           |        
               | deltaA  30                            |        
               | random  yes                           |        
            -->| TORUS                                 |        
               | origin  5 9 17                        |        
               | axe     0 0 1                         |        
               | Radius  8                             |        
               | radius  3                             |        
               | aniso   0.8                           |        
               | lambda1 23.5                          |        
               | deltaL  0.4                           |        
               | deltaA  20                            |        
               | random  no                            |        
            -->| CUBE                                  |        
               | p0      0 0 0                         |        
               | p1      10 10 10                      |        
               | axe     1 0 0                         |        
               | aniso   0.1                           |        
               | lambda1 1.0                           |        
               | deltaL  0.1                           |        
               | deltaA  30                            |        
               | random  yes                           |        
            -->| PARALLELEPIPEDE                       |        
               | origin  0 0 0                         |        
               | v1      1 0 0                         |        
               | v2      0 1 0                         |        
               | L1      4                             |        
               | L2      8                             |        
               | L3      6                             |        
               | axe     1 0 0                         |        
               | aniso   0.1                           |        
               | lambda1 1.0                           |        
               | deltaL  0.1                           |        
               | deltaA  30                            |        
               | random  no                            |        
               +---------------------------------------+        
     fileout : output volume sequence file                      
     sx,sy,sz: voxel size [default=1.0,1.0,1.0]                 
----------------------------------------------------------------

AimsSparseMatrixToDense.py

Usage: AimsSparseMatrixToDense.py [options]

Read a sparse matrix (*.imas), write it as a dense matrix (any volume format).
The dense matrix must fit in memory since it is transformed in memory first.

Options:
  -h, --help            show this help message and exit
  -i INPUT, --input=INPUT
                        input sparse matrix file
  -o OUTPUT, --output=OUTPUT
                        output dense matrix, written as a 2D volume

AimsSphereDistribution


    AimsSphereDistribution
    ----------------------

Output a file with coordinates of discrete spheric distribution with any number
of directions.

Options :

-d | --direction <S32>
    number of directions

[ -o | --output <string> ]
    output file name (default: standard output)

[ -s | --steps <S32> ]
    maximum number of minimization steps (default 1000)

[ -r | --radius <DOUBLE> ]
    radius of the sphere (default : 1)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSplitArray


    AimsSplitArray
    --------------

Split one array image in print-tip images

Options :

-i | --input <file name (read only): volume of U16>
    array image

-o | --output <filename: volume of S16>
    name of output pseudo volume

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSplitRgb


    AimsSplitRgb
    ------------

Split an AimsData<AimsRGB> into 3 AimsData<byte> files

Options :

-i <string>
    input RGB data

[ -o <string> ]
    output data

[ -t <string> ]
    output data type [default: U8]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSpmNormalizationConvert.py

Usage: AimsSpmNormalizationConvert.py [options]

Reads the affine part of a SPM normalization file (_sn.mat) and converts it to
an AIMS .trm file.

Options:
  -h, --help            show this help message and exit
  -i FILE, --input=FILE
                        SPM normalization file (*_sn.mat)
  -s SOUREFILE, --source=SOUREFILE
                        source image which has been used for normalization,
                        but not resampled in the template space
  -o TRMFILE, --output=TRMFILE
                        output transformationfile *.trm
  -d DESTREF, --destref=DESTREF
                        set destination referential name/UUID. Default: none
  --srcref=SRCREF       set source referential name/UUID. Default: try to
                        guess it from source image

AimsSubSampling


    AimsSubSampling
    ---------------

Image subsampling

Options :

-i | --input <string>
    Input image to subsample

[ -rx <S32> ]
    X number of voxels to aggregate [default = 1]

[ -ry <S32> ]
    Y number of voxels to aggregate [default = 1]

[ -rz <S32> ]
    Z number of voxels to aggregate [default = 1]

[ -n <S32> ]
    Number of voxels to aggregate in X and Y directions [default = 2](this
    option is obsolete and only provided for compatibility purpose)

[ -t <string> ]
    Subsampling type : med[ian], mea[n], min[imum], max[imum], 
    maj[ority], dif[ference], sum, notnullmean [default = median]. Modes may
    also
    be specified as order number: 0=median, 1=mean, etc.

-o | --output <string>
    Output subsampled image

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSubTensor


----------------------------------------------------------------
AimsSubTensor [-h[elp]]                                         
               -i[nput] <filein>                                
               -o[utput] <fileout>                              
              [-x <xmin> -y <ymin> -z <zmin>                    
               -X <xmax> -Y <ymax> -Z <zmax>]                   
              [-m<ask> <bucket>]                                
              [-a[scii]]                                        
----------------------------------------------------------------
Extracting a subpart from a DtiTensor bucket                    
----------------------------------------------------------------
     filein         : source tensor bucket                      
     fileout        : destination bucket of sub-dtitensor       
                      generates    fileout.bck                  
     xmin,ymin,zmin : inferior point of the box sub-part        
     xmax,ymax,zmax : superior point of the box sub-part        
     bucket         : Void bucket mask                          
     ascii          : write in ascii mode rather than binary    
                      [default=binary]                          
----------------------------------------------------------------

AimsSubVolume


    AimsSubVolume
    -------------

Carve a subvolume in the input volume 

Options :

-i | --input <string>
    input data

[ -x | --firstx <vector of S32> ]
    first x coordinate (default 0)

[ -y | --firsty <vector of S32> ]
    first y coordinate (default 0)

[ -z | --firstz <vector of S32> ]
    first z coordinate (default 0)

[ -t | --firstt <vector of S32> ]
    first t coordinate (default 0)

[ -X | --lastx <vector of S32> ]
    last x coordinate (default SizeX-1)

[ -Y | --lasty <vector of S32> ]
    last y coordinate (default SizeY-1)

[ -Z | --lastz <vector of S32> ]
    last z coordinate (default SizeZ-1)

[ -T | --lastt <vector of S32> ]
    last t coordinate (default SizeT-1)

[ -s | --split <boolean> ]
    split a 4D volume into a series of 3D volumes. Output filenames will be
    appended with a timestep number.

[ -l | --lap <boolean> ]
    take X,Y,Z and T as dimensions instead of coordinates)

-o | --output <vector of string>
    output data

[ -motion <boolean> ]
    Write motions whole_TO_subvolume and inverse (default=no)

[ -mdir <string> ]
    Motion name : whole_TO_subvolume

[ -minv <string> ]
    Motion name : subvolume_TO_whole

[ --singleminf <boolean> ]
    Only write .minf meta-header on the first sub-volume (useful when writing a
    series)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSulciVoronoi.py

Usage: AimsSulciVoronoi.py [options]

Voronoi diagram of the sulci nodes regions, in the grey matter, and extending
to the whole 3D space

Options:
  -h, --help            show this help message and exit
  -g LGW, --greywhite=LGW
                        left grey/white mask
  -o VORONOI, --output=VORONOI
                        output voronoi diagram volume
  -f GRAPH, --folds=GRAPH
                        sulci graph file

AimsSulcusSPAM


    AimsSulcusSPAM
    --------------

Surface-based SPAM statistical map for sulcus

Options :

-t | --texture <string>
    object definition

-s | --sulci_spam <string>
    output SPAM texture

-m | --mesh <string>
    input mesh

-o | --output <string>
    output mesh

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSumFrame


    AimsSumFrame
    ------------

Compute The sum of the dynamic series :for a PET file, use AimsSumPETImage

Options :

-i | --input <file name (read only): { Volume of DOUBLE, Volume of FLOAT,
    Volume of S16, Volume of S32, Volume of S8, Volume of U16, Volume of U32,
    Volume of U8 }>  input series <dynamic series>

[ -s | --startframe <S32> ]
    start frame < between 1 and maxFrame >

[ -e | --endframe <S32> ]
    end frame < between 1 and maxFrame >

[ -b | --byframe <boolean> ]
    (to enforce frame by frame computation)

-o | --output <string>
    output average volume

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSumPETFrame


    AimsSumPETFrame
    ---------------

Compute The sum (average) of the dynamic PET series

Options :

-i | --input <file name (read only): { Volume of DOUBLE, Volume of FLOAT,
    Volume of S16, Volume of S32, Volume of S8, Volume of U16, Volume of U32,
    Volume of U8 }>  input series <dynamic series>

[ -s | --startframe <S32> ]
    start frame < between 1 and maxFrame >

[ -e | --endframe <S32> ]
    end frame < between 1 and maxFrame >

[ -b | --byframe <boolean> ]
    (to enforce frame by frame computation)

-o | --output <string>
    output average volume

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSumSparseMatrix


    AimsSumSparseMatrix
    -------------------

Sum Sparse Matrices

Options :

[ -i <vector of string> ]
    input sparse matrices filenames

-o <string>
    output sparse matrix: sum of the input matrices

[ -fmt <string> ]
    output sparse format: binary or ascii, default = binar

[ -verbose <boolean> ]
    show as much information as possible

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsT1mapVFA.py

Usage: AimsT1mapVFA.py [options]

Processing of Cortical thickness attributes in Cortical Folds Graph

Options:
  -h, --help            show this help message and exit
  -t T1_LOWANGLE, --t1_low=T1_LOWANGLE
                        first GRE T1 with lower angle
  -u T1_HIGHANGLE, --t1_high=T1_HIGHANGLE
                        second GRE T1 with higher angle
  -a BAFI_AMPL, --bafi_amplitude=BAFI_AMPL
                        BAFI, amplitude map
  -p BAFI_PHASE, --bafi_phase=BAFI_PHASE
                        BAFI, phase map
  -o OUTPUT_T1MAP, --output=OUTPUT_T1MAP
                        output T1 mapping image
  -s SMOOTH_TYPE, --smoothtype=SMOOTH_TYPE
                        extrapolation / smoothing type for B1 map. allowed
                        values: nearest, linear, masked_linear, polynomial,
                        median, dilated. default: linear
  -g GAUSSIAN, --gaussian=GAUSSIAN
                        additional gaussian smoothing for the B1 correction
                        map. default: 0mm: not applied
  --inv                 invert T1 map image to look like a T1-weighted
  --out_b1map_raw=OUT_B1MAP_RAW
                        output the raw B1 map in the specified file
  --out_b1map_median=OUT_B1MAP_MEDIAN
                        output the B1 map with median filter in the specified
                        file (if median option is used)
  --out_b1map=OUT_B1MAP
                        output the final B1 map in the specified file

AimsT2BasedCorrectionEpi


    AimsT2BasedCorrectionEpi
    ------------------------

T2 based correction of echoplanar distortions in DW MR image
Base on a model of geometric distortion characterized by:
- a scaling S,
- a translation T0,
- a shearing T1

Options :

-i <file name (read only): volume of S16>
    T2+DW image

-d <string>
    Description file

-o <filename: volume of S16>
    Corrected T2+DW image

[ -divider <S32> ]
    divider for subresolution calculations (default=1)

[ -levels <S32> ]
    number of graylevels in MI calculations (default=64)

[ -smoothing <string> ]
    pdf smoothing deriche/discrete (default=discrete)

[ -sigma <FLOAT> ]
    discrete : gaussian mask size (default=3)
    deriche  : gaussian std dev. (default=3.0mm)

[ -deltaS <FLOAT> ]
    variation of S (default=0.05)

[ -deltaT0 <FLOAT> ]
    variation of T0 (default=1.00)

[ -deltaT1 <FLOAT> ]
    variation of T1 (default=0.01)

[ -error <FLOAT> ]
    tolerance on results (default=0.005)

[ -memMap <boolean> ]
    memory mapping activated (obsolete, automatic)

[ -parameters <string> ]
    (S,T0,T1) parameter text file name [default=not saved]

[ -verbose <boolean> ]
    show as much information as possible

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsTCat


    AimsTCat
    --------

Concatenates files along time.
Works on homogen input data (volumes of S16, ...). Currently supports:
Bucket of VOID
Mesh of VOID
Mesh2 of VOID
Mesh4 of VOID
Texture of FLOAT
Texture of POINT2D
Texture of POINT2DF
Texture of S16
Texture of U32
Volume of CDOUBLE
Volume of CFLOAT
Volume of DOUBLE
Volume of FLOAT
Volume of POINT3DF
Volume of RGB
Volume of RGBA
Volume of S16
Volume of S32
Volume of S8
Volume of U16
Volume of U32
Volume of U8

Options :

-o | --output <string>
    output data

-i | --input <vector of string>
    input files

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsTMSCone.py

Usage: AimsTMSCone.py [options]

Creates a cone or other mesh representing the TMS active zone at the specified
target position along the head mesh

Options:
  -h, --help            show this help message and exit
  -i HEADMESHFILE, --input=HEADMESHFILE
                        input head mesh
  -o CONEFILE, --output=CONEFILE
                        output mesh
  -s STIMPOINT, --stimpoint=STIMPOINT
                        stimulation position in mm on head or cortex (3 float
                        numbers)
  -r BASERADIUS, --radius=BASERADIUS
                        stimulation cone base radius
  -d DEPTH, --depth=DEPTH
                        stimulation cone depth
  -n NORMALRADIUS, --normalradius=NORMALRADIUS
                        radius around stimulation point to average normal
                        [optional, default=20]
  -m NORMALMESH, --normalmesh=NORMALMESH
                        output mesh for the normal line (just for
                        visualization purpose) [optional]
  -t TARGETLINEMESH, --targetlinemesh=TARGETLINEMESH
                        output mesh for the target-head projection line, which
                        might be slightly different from the normal. If the
                        target is specified on the head, this line is by
                        defninition the normal. [optional]
  -b BRAIN, --brain=BRAIN
                        brain (or grey/white cortex) mask [optional, -z option
                        needed]
  -c CORTEXVALUE, --cortex=CORTEXVALUE
                        cortex value in grey/white mask image, [default: all
                        non-zero]
  -z STIMZONE, --zone=STIMZONE
                        stimulation zone output filename (.bck) [optional, -b
                        option needed]
  -w WRITERESULTS, --writeresults=WRITERESULTS
                        output text file where to write results (points and
                        directions) [optional]

AimsTMStarget


    AimsTMStarget
    -------------

Creates texture target for TMS aiming

Options :

-i | --input <string>
    input mesh file (head)

-o | --output <string>
    output target texture file

[ -n <U32> ]
    Neighbourhood size for the target position estimation
    [default = 10]

-l | --landmarks <string>
    landmarks positions file

[ --ascii <boolean> ]
    write texture file in ASCII mode 
    [default=binary]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsTalairachTransform


    AimsTalairachTransform
    ----------------------

Compute talairach transform from talairach base coordinates and a mask

Options :

[ -apc <string> ]
    apc file transformation

[ -o <string> ]
    Output transformation file

[ -m <string> ]
    Mask

[ -ns <boolean> ]
    No scale factor is applied, single rotation around AC, no talairach
    coordinates

[ -p <string> ]
    Roi graph containing points placed on the extremities of the brain

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsTensor2Bucket


----------------------------------------------------------------
AimsTensor2Bucket [-h[elp]]                                     
                   -i[nput] <filein>                            
                   -o[utput] <fileout>                          
                   -m[ask] <brain>                              
                  [-a[scii]]                                    
                  [-s[upplement]]                               
                  [-r[eplace]]                                  
                  [-u[ncorrected]]                              
----------------------------------------------------------------
Transformation of 4D tensor image to tensor bucket              
----------------------------------------------------------------
     filein     : source echo data (GIS)                        
     fileout    : destination bucket of dtitensor               
                  generates    fileout.bck                      
     brain      : U8 mask of the brain or white matter          
     ascii      : save bucket in ASCII mode                     
     supplement : save also files fileout_traceTC.ima           
                                  fileout_traceEV.ima           
                                  fileout_VR.ima                
                                  fileout_FA.ima                
                                  fileout_dir.ima               
                                  fileout_dirRGB.ima            
     replace    : when a point is NOT_POSITIVE_MATRIX, replace  
                  by an isotropic tensor which mean diffusivity 
                  is estimated on the N26 neighborhood of the   
                  point rather than the mean diffusivity equal  
                  to traceTC / 3.0                              
     uncorrected: let traceEV and traceTC not corrected         
                  (they may become negative with noise)         
----------------------------------------------------------------

AimsTensorExtract


----------------------------------------------------------------
AimsTensorExtract [-h[elp]]                                     
                   -i[nput] <filein>                            
                  [-o[utput] <fileout>]                         
                   -x[dim] <dimX>                               
                   -y[dim] <dimY>                               
                   -z[dim] <dimZ>                               
----------------------------------------------------------------
Extract anisotropy,trace,directions from dtitensor bucket       
----------------------------------------------------------------
     filein     : source dtitensor bucket                       
     fileout    : destination base file name                    
                                  fileout_traceTC.ima           
                                  fileout_traceEV.ima           
                                  fileout_VR.ima                
                                  fileout_FA.ima                
                                  fileout_dir.ima               
                                  fileout_dirRGB.ima            
                  [default=filein]                              
     dimX,dimY,dimZ : dimensions of output images               
----------------------------------------------------------------

AimsTensorSNR


----------------------------------------------------------------
AimsSNR -i[nput] <filein>                                       
       [-v[oi] <voi>]                                           
       [-x <X> -y <Y> -z <Z> -R <R>]                            
       [-o[utput] <fileout>]                                    
       [-h[elp]]                                                
----------------------------------------------------------------
SNR of a VOI in a tensor image                                  
----------------------------------------------------------------
     filein  : dtitensor bucket file                            
     voi     : U8 data file of the V.O.I.                       
     X,Y,Z   : Point3d center of a spherical ROI                
     R       : radius of spherical ROI                          
     fileout : output file [default=stdout]                     
----------------------------------------------------------------

AimsTex2Graph


    AimsTex2Graph
    -------------

Makes a roi graph from a mesh and a texture of labels

Options :

-t | -texture <file name (read only): texture of S16>
    input label (short) texture

-m | -mesh <file name (read only): Mesh of VOID>
    input mesh

-o | -output <string>
    output graph

[ -T | -Time | -time <U32> ]
    make graph from time T of input texture

[ -c | -conversion <string> ]
    conversion table  (short label to  name)

[ --reverse <boolean> ]
    flip conversion table (name to short label)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsTex2Vol


    AimsTex2Vol
    -----------

Compute cortical parcellation

Options :

-i | --input <string>
    Cortical segmentation

-m | --mesh <file name (read only): Mesh of VOID>
    input sulcal mesh

-t | --texture <string>
    input segmentation texture

-g <S32>
    cortical label [default=0]

-o | --output <string>
    output cortical parcellation

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsTexture2Primal


-------------------------------------------------------------------------
AimsTexture2Primal       -i[nput] <input_texture>                        
                         -v[olume] <input_volume>                        
                         -M[esh]  <input mesh>                           
                         -F[lat]  <input inflated_mesh>                  
                         -b[egin] <begin_scale>                          
                         -e[nd] <end_scale>                              
                         -d[t] <scalespace sample step>                  
                         --log <logarithm scale>                         
                         [-H[max]    <texture_threshold> ]               
                         [-p[primal] <output_primal>]                    
                         [-g[raph]   <output_graph>]                     
                         -B[lobs]   <output_blobs_texture>               
                         -o[utputss]   <output_scalespace_textur>        
                         [-g[raph]   <output_graph>]                     
                         [-s[urface] <surface_type>]                     
                         [-G[row]    <grow_mode>]                        
                         [-t[ranslation] <coef_translation>]             
                         [-m[indt] <min scalespace sample step>]         
                         [-W[max] <Weight threshold>                  
                         [-S[moothstep] <smooth step for the edp>]       
                         [-c[onvexity] ]                                 
                         [-h[elp]]                                       
-------------------------------------------------------------------------
 Build the primal sketch of a texture using 2D geodesic diffusion        
-------------------------------------------------------------------------
      begin_scale                 :  First scale in the scale space      
      end_scale                   :  Last  scale in the scale space      
      scale space sample step     :  Max sample step in the scale space  
      min scale space sample step :  Min sample step in the scale space  
                                     <default = scale space sample step> 
      Smooth step for the edp     :  Time step for te edp (depending from the triangulation)
                                     <default = automatic>               
      Weight  threshold         :    (Absolute) threshold for the laplacian weight estimate
                                     <default = 0.1>                       
      Texture threshold           :  (Absolute) threshold for the textures values
                                     <default = auto (max of the texture)>
      Convexity                   :  Grey level blob correspond to:      
                                         -local minima (convexity = -1)  
                                         -local maxima (convexity =  1)  
 					<default = -1>                      
      output_primal               :  Make also the corresponding primal sketch graph 
                                     (Scale Space Blob graph) <default = not used>           
      output_graph                :  Make also the corresponding  graph  
                                     (Grey Level Blob graph)  <default = not used>           
      surface_type                :  Tore (default) or surface           
      coef_translation            :  Link between the scale and the distance to the mesh
      grow_mode                   :  Mesh growing mode along scales: scale (default),
                                     translate, or pushnormal            
-------------------------------------------------------------------------

AimsTextureAverage


-------------------------------------------------------------------------
AimsTextureAverage -f[loat_texture] <input_float_texture>]              
                   -o[utput <output_mesh>]                               
                   --binary                                              
                   --max                                              
                   --min                                              
                  [-h[elp]]                                              
-------------------------------------------------------------------------
 Compute the average of a time-serie texture                             
-------------------------------------------------------------------------
     input_float_texture : input time-serie texture                  
     output_texture      : output mean texture                           
     binary              : binarise the input texture                    
     max                 : compute the maximum instead of the mean input texture                    
     min                 : compute the minimum instead of the mean input texture           
-------------------------------------------------------------------------

AimsTextureDerivative


    AimsTextureDerivative
    ---------------------

Compute first and second derivative  of the input texture

Options :

-i | --input <string>
    texture definition

-m | --mesh <string>
    mesh file

-o | --output <string>
    output texture

-p | --pinv <string>
    pinv_filename

[ -T | --Time <S32> ]
    time point [default: 0]

[ --curvature <boolean> ]
    curvature

[ --Lvv <boolean> ]
    means certainly something

[ --Lw <boolean> ]
    means certainly something

[ --laplacian | --laplacien <boolean> ]
    means certainly something

[ --div <boolean> ]
    means certainly something

[ --all <boolean> ]
    implies all of --curvature, --Lvv, --Lw, --laplacian flags

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsTextureDilation


    AimsTextureDilation
    -------------------

Dilation of an image (binary or grey level) painted on a triangulation.
Input texture of 'short int' are eroded with binary structuring element.
The 'background label' corresponds to the label of the background (default =
0).
The 'forbidden label' corresponds to the label out of the domain (default =
-1).
Input texture of 'float' are eroded with the min function as structuring
element

Options :

-i | --input <string>
    input mesh file

-t | --texture <string>
    object definition texture

-o | --output <string>
    output texture file (labelled opening)

-s | --size <FLOAT>
    dilation size (in mm)

[ -b | --background <S32> ]
    background label

[ -f | --forbidden <S32> ]
    forbidden label

[ --connexity <boolean> ]
    euclidean or mesh connexity [default=euclidean]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsTextureErosion


    AimsTextureErosion
    ------------------

Erosion of an image (binary or grey level) painted on a triangulation.
Input texture of 'short int' are eroded with binary structuring element.
The 'background label' corresponds to the label of the background (default =
0).
The 'forbidden label' corresponds to the label out of the domain (default =
-1).
Input texture of 'float' are eroded with the min function as structuring
element

Options :

-i | --input <string>
    input mesh file

-t | --texture <string>
    object definition texture

-o | --output <string>
    output texture file (labelled opening)

-s | --size <FLOAT>
    erosion size (in mm)

[ -b | --background <S32> ]
    background label

[ -f | --forbidden <S32> ]
    forbidden label

[ --connexity <boolean> ]
    euclidean or mesh connexity [default=euclidean]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsTexturePrimalSketch


    AimsTexturePrimalSketch
    -----------------------

ScaleSpace et grey level blobs d'une surface/texture au format float

Options :

-t | --inputT <string>
    inputTexture

-o <string>
    output primal sketch graph

-m | --inputM <string>
    inputMesh

-os | --output-scales <string>
    scale space texture filename

-ob | --output-blobs <string>
    blobs texture filename

[ -t1 | --scalemin <FLOAT> ]
    minimum scale (default=1.0)

-t2 | --scalemax <FLOAT>
    maximum scale

[ -dt | --deltat <FLOAT> ]
    time step (default=0.05)

[ -mX | --auxmesh <string> ]
    auxilliary mesh (for the rendering)

[ -sj | --subject | --subject <string> ]
    subject name (default : inputImage)

[ --trans <string> ]
    Transformation matrix to Talairach space

[ -iP <U32> ]
    Intersection condition for grey-level blobs matching across scales

[ -f <FLOAT> ]
    filter out blobs whose tvalues are under (default=1.0)

[ -l <string> ]
    texture latitude

[ -L <string> ]
    texture longitude

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsTextureRegularization


    AimsTextureRegularization
    -------------------------

Regularize the texture

Options :

-t | --texture <string>
    texture file

-o | --output <string>
    output texture

[ -r | --ratio <FLOAT> ]
    proportion (%) of point to be thresholded 

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsTextureScaleSpace


    AimsTextureScaleSpace
    ---------------------

ScaleSpace d'une surface/texture

Options :

-i1 | --input1 <string>
    inputTexture

-i2 | --input2 <string>
    inputMesh

-o | --output <string>
    output filename pattern

-tm | --scalemax <FLOAT>
    maximum scale

-dt | --deltat <FLOAT>
    time step

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsTextureSmoothing


    AimsTextureSmoothing
    --------------------

Geodesic smoothing of the input texture (Laplacian: heat equation)

Options :

-i | --input <file name (read only): texture of FLOAT>
    input object definition texture

-o | --output <filename: texture of FLOAT>
    output texture file

-m | --mesh <file name (read only): Mesh of VOID>
    mesh file

[ -S | --Source | --source <file name (read only): texture of FLOAT> ]
    input source definition texture

[ -s | --sigma <FLOAT> ]
    equivalent gaussian sigma. Specify either sigma or duration.

[ -d | --duration <FLOAT> ]
    Diffusion process duration. Either sigma or duration must be specified.

[ -t | --timestep <FLOAT> ]
    timestep. Default = automatic estimation

[ -T | --Time | --time <S32> ]
    Timepoint in the input texture to be smoothed. Default: 0

[ -W | --Wmax <FLOAT> ]
    weight ratio threshold. Default: 0.98

[ -H | --Hmaw <FLOAT> ]
    output threshold (max of the output texture). Default: 10000

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsTextureThreshold


    AimsTextureThreshold
    --------------------

Threshold on texture  (each time serie is thresholded)

Options :

-i | --input <string>
    origin file

-o | --output <string>
    output file

-m | --mode <string>
    mode that can be:
    lt --> lower than
    le --> lower or equal to
    gt --> greater than
    ge --> greater or equal to
    eq --> equal to
    di --> differ
    be --> between
    ou --> outside

-t <FLOAT>
    first threshold

[ -u <FLOAT> ]
    second threshold (if any)

[ -b | --binary <boolean> ]
    returns a short binary texture (background : 0 ; object : 1)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsTextureVoronoi


    AimsTextureVoronoi
    ------------------

Compute the Voronoi diagram of the input (short int) seed texture

Options :

-m | --mesh <file name (read only): Mesh of VOID>
    input_mesh

-o | --output <filename: texture of S16>
    output voronoi diagram texture

-t | --texture <file name (read only): texture of S16>
    seeds texture definition (short int)

[ -T | --Time <S32> ]
    time step <default = 0>

[ -b | --background <S16> ]
    background value <default = 0>

[ -f | --forbidden <S16> ]
    value out of the domain <default = -1>

[ -s | --step <FLOAT> ]
    step size <default = infinity>

[ -c | --connexity | --connectivity <boolean> ]
    connectivity or geodesic euclidean distance <default: euclidean>

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsThreshold


    AimsThreshold
    -------------

Threshold on data

Options :

-i | --input <file name (read only): { Volume of DOUBLE, Volume of FLOAT,
    Volume of S16, Volume of S32, Volume of S8, Volume of U16, Volume of U32,
    Volume of U8 }>  input file

-o | --output <string>
    output file

[ -m | --mode <string> ]
    mode that can be:
    lt   --> lower than
    le   --> lower or equal to
    gt   --> greater than
    ge   --> greater or equal to
    eq   --> equal to
    di   --> differ
    be   --> between
    beel --> between, exclude lower bound
    beeh --> between, exclude higher bound
    bee  --> between, exclude both bounds
    ou   --> outside
    ouil --> outside, include lower bound
    ouih --> outside, include higher bound
    oui  --> outside, include both bounds
    [default: ge]

-t | --threshold1 <FLOAT>
    first threshold

[ -u | --threshold2 <FLOAT> ]
    second threshold

[ -p <boolean> ]
    thresholds are expressed in percentage of voxel value: threshold =
    min+(max-min)*(percentage/100)

[ -b | --binary <boolean> ]
    returns a short binary data [default: false]

[ --bg <FLOAT> ]
    background value set on thresholded out voxels in non-binary mode [default:
    0]

[ --fg <FLOAT> ]
    foreground value set on thresholded in voxels in binary mode [default:
    32767]

[ --clip <boolean> ]
    clip thresholded-out values [default: false]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsTopologicalClassification


    AimsTopologicalClassification
    -----------------------------

Topological classification of each point of a labeled image

Options :

-i | --input <file name (read only): { Bucket of S16, Bucket of VOID, Volume of
    S16, Volume of S32, Volume of S8, Volume of U16, Volume of U32, Volume of
    U8 }>  input volume or bucket

-o | --output <string>
    output volume or bucket

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsVFilter


----------------------------------------------------------------
AimsVFilter -i[nput] <filein>                                   
            -o[utput] <fileout>                                 
            [-m[asksize] <size>]                                
            [-t[ype] <algo>]                                    
            [-h[elp]]                                           
----------------------------------------------------------------
apply a V-Filter to an image                                    
----------------------------------------------------------------
     filein  : origin file                                      
     fileout : output file                                      
     size    : mask size [default=2]                            
     algo    : o -> optimized    n -> non optimized  [default=o]
----------------------------------------------------------------

AimsValidateFit


    AimsValidateFit
    ---------------

A test program I think, nothing useful

Options :

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsVectorFieldToMesh


    AimsVectorFieldToMesh
    ---------------------

Converts a vector field volume to a mesh of arrows

Options :

-i | --input <string>
    input vector field (either one RGB image or a 4D image with 3 components)

-o | --output <string>
    output mesh

[ -s <FLOAT> ]
    scale factor (default=normalization)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsVeinExtraction


    AimsVeinExtraction
    ------------------

Semi-automatic vein extraction using global minimum energy path for active
contours with geodesics

Options :

-i <string>
    Input image

-o <string>
    Output segmented image

[ -m <string> ]
    Input image modality (MRI, Other)

[ -b <vector of FLOAT> ]
    First point on vein

[ -e <vector of FLOAT> ]
    Last Point on vein

[ -d <FLOAT> ]
    vein diameter (default : 5 mm)

[ -w <S32> ]
    Border with for twisted veins (default : 15 voxels )

[ -li <boolean> ]
    lowervalue of image is inaccessible (default : false)

[ -t <string> ]
    Voi type : arg, image (default : arg )

[ -wi <boolean> ]
    using whole image (default : no )

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsVoiStat


    AimsVoiStat
    -----------

Compute ordinary stat from a RoiArg and and Image (Warning:--selection all and
--voitype gtm are incompatibles) (Warning: DOUBLE images are converted to FLOAT
so there si a possible loss of information)

Options :

-i | --input <string>
    input dynamic data

-v | --voi <string>
    file containing roi information see (--voitype)

-o | --output <string>
    output

[ -d | --displ <string> ]
    displacement file from functional image to ROI. default val : Identity

[ -s | --selector <string> ]
    user defined selector file name

[ -l | --list <boolean> ]
    list of available template selectors

[ --hierarchy <string> ]
    nomenclature file

[ --selection <string> ]
    template selector name available selectors may be listed (switch -l) OR
    "all" to disable selection mode

[ --voitype <string> ]
    subselector for voi file type arg (for arg format), image (for image
    format), gtm (for composite gtm arg file and roi arg file)
    [Default: arg]

[ --byframe <boolean> ]
    set frame by frame computation mode

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsVolumeExtract


    AimsVolumeExtract
    -----------------

#============================================================================#
#                              WORK IN PROGRESS                              #
#        Only Soma-IO formats (currently GIS) are supported for now          #
#============================================================================#
Writing of volumes with various sources.
This command allows one to create a volume of given size, which may be filled
with existing data, or be entirely blank. It also allows writing exisiting data
in a region of an existing volume.
It is thus possible to :
	- Write a blank volume
	- Extend the dimensions of a volume (same as AimsOverVolume)
	- Crop a volume (same as AimsSubVolume)
At least one of -i and -s[x|y|z|t] option is required. See additional
descriptions to understand the usage of parameters.

Options :

-o <string>
    Output filename to be written.
    If volume dimensions are given, it is created on disk, else if the output
    file already exist, data are written in it

[ -r <string> ]
    Reference volume
    Its dimension and voxel size will be used for the output volume in the case
    of empty volume creation, when no input is given. They will be overriden by
    the use of -od and -ov options.

[ -od <vector of S32> ]
    Dimension of output volume.
    If one of the output size parameters is given, eventual existing volume is
    crushed. If it is not given and a new volume is created, default value is
    1. If it is not given and we use an existing output volume, volume's size
    is used.

[ -ov <vector of FLOAT> ]
    Voxel size of output volume.
    Only used if an output volume is created (default value is 1). If an
    existing volume is used, we keep its voxel size.

[ -i <string> ]
    Source volume.
    It contains the data used to fill the output volume. If none is given, the
    output volume is entirely blank.
    Partial access options can be used on reading, see further.

[ -ir <vector of S32> ]
    Size of input region to read.
    This is a parameter relative to partial reading. It specifies the region of
    input volume we want to extract and write in output.
    If one of the partial reading parameters is given, default value is the
    size of the full volume.

[ -ip <vector of S32> ]
    Position of input region to read.
    This is a parameter relative to partial reading. It specifies the region of
    input volume we want to extract and write in output.
    If one of the partial reading parameters is given, default value is the
    size of the full volume.

[ -op <vector of S32> ]
    Position of data in output volume.
    This is a parameter relative to writing of data. It specifies the position
    of input data in the output volume (which can be larger).
    Default value is 0 (no translation).

[ -t <string> ]
    Data type of output volume
    Only use this when no input file is given. Data Type is described by a
    string : U8, S16, FLOAT, RGB...
    If both a data type and an input file are given, -t option is not used
    If both a data type and an existing output file are given, -t option is not
    used.

[ -extract <boolean> ]
    UnderVolume mode.
    If this option is used, the chosen input region is extracted and written in
    output. No extension is done.
    Needs an input file. Do not use with output options (-od,-op,...)

[ --debugLevel | -d <S32> ]
    Set debug information level (default = 0)

[ --verbose | -v [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsVolumeToTexture.py

Usage: AimsVolumeToTexture.py [options]

Project volume voxels valus on a mesh into a texture. Each vertex simply gets
the volume value at its position.

Options:
  -h, --help            show this help message and exit
  -i INPUT, --input=INPUT
                        input volume
  -m MESH, --mesh=MESH  mesh file
  -o OUTPUT, --output=OUTPUT
                        output texture file
  -t TRANSFORM, --transform=TRANSFORM
                        optional transformation file between the volume and
                        mesh spaces

AimsVoronoi


    AimsVoronoi
    -----------

Construct a Voronoi diagram from labelled seeds

Options :

-i | --input | -input <file name (read only): { Volume of S16, Volume of S32,
    Volume of S8, Volume of U16, Volume of U32, Volume of U8 }>  input seeds
    volume filename

-o | --output | -output <string>
    output Voronoi diagram filename (same voxel type as input)

[ -d | --domain | -domain <DOUBLE> ]
    value of the domain where to propagate the diagram [default=0]

[ -f | --forbidden | -forbidden <DOUBLE> ]
    value of the outside (forbidden) of the domain [default=-1]

[ -x | --xmask | -xmask <S32> ]
    X size of the distance mask [default=3]

[ -y | --ymask | -ymask <S32> ]
    Y size of the distance mask [default=3]

[ -z | --zmask | -zmask <S32> ]
    Z size of the distance mask [default=3]

[ -F | --factor | -Factor <FLOAT> ]
    chamfer multiplication factor [default=50]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsZCat


    AimsZCat
    --------

concatenates volumes (along Z axis), meshes or buckets

Options :

-i <list of string>
    input files (1 minimum)

-o <string>
    Output file name

[ --memmap <boolean> ]
    read in Memory Mapping mode (obsolete, automatic)

[ --nocheckvs <boolean> ]
    Don't check if voxel sizes of all volumes to concatenate match

[ --vsx <FLOAT> ]
    Force voxelsize X value

[ --vsy <FLOAT> ]
    Force voxelsize Y value

[ --vsz <FLOAT> ]
    Force voxelsize Z value

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


EcatVolMIProj

bin/EcatVolMIProj: invalid option -- 'h'
 usage : EcatVolMIProj -i(nput) -o(utput) [-t thet]a  [-a #angles], default=32]

                       -i input file in 3dSinogram format
                       -o output file in PetProjection format (*.p)
                       -t polar angle in radian, default = 0
                       -a number of projection angles, default = 32

EcatVolReverse

bin/EcatVolReverse: invalid option -- 'h'
 usage : EcatVolReverse -i(nput) -o(utput) [-x(reverse), -y(reverse), -z(reverse)]

cartoFSLmatToTrm.py

Usage: cartoFSLmatToTrm.py [options]

Transforms a FSL registration matrix (.mat, but _not_ a matlab file) into an
AIMS .trm transformation file, and converts coordinates systems from FSL to
AIMS.

Options:
  -h, --help            show this help message and exit
  -i INPUT, --input=INPUT
                        input .mat FSL transformation
  -o OUTPUT, --output=OUTPUT
                        output .trm AIMS transformation
  -s SOURCE, --source=SOURCE
                        transformation source image
  -d DESTINATION, --destination=DESTINATION
                        transformation destination image

cartoGraphAddAttributeFromCsv.py

Usage: cartoGraphAddAttributeFromCsv.py [options]

Add an attritute to some nodes of a graph. The attribute stem from a csv file
with an header. Each line of this file is a pair of node-name value

Options:
  -h, --help     show this help message and exit
  -i FILE        Input graph
  -o FILE        Output graph (default=out.arg)
  -j FILE        Input csv file
  -k STRING      graph key attribute: the attribute name which identifies the
                 graph nodes (default=name)
  -l STRING      graph value attribute: the attribute name of the graph nodes
                 that will be used to store the value,
                 (default=custom_num_val)
  -m STRING|INT  table (csv) column name|number which contains keys to be
                 matched with attribute name of the graph (default=0, first
                 column)
  -n STRING|INT  csv column name|number which contains values to be set with
                 attribute name of the graph (default=1, second column)
  -q, --quiet    don't print status messages to stdout

cartoGraphAddAttributeFromCsv.py -i input_fold_graph.arg -j stats-values.csv

cartoGraphCat.py

Usage: cartoGraphCat.py [options]

Graphs concatenation

Options:
  -h, --help            show this help message and exit
  -o OUTPUT, --output=OUTPUT
                        output graph
  -i FILENAME, --input=FILENAME
                        input graph(s)

cartoGraphTransform.py

Usage: cartoGraphTransform.py [options]

Apply transformations to ROI graph nodes. Several transformations can apply to
different regions specified by their name. Currently only ROI bucket graphs
are handled, and no resampling is done (each voxel is transformed with no more
processing, which may result in holes and/or unconnected regions if scaling
factors are superior to 1.)

Options:
  -h, --help            show this help message and exit
  -i INPUT, --input=INPUT
                        input graph
  -o OUTPUT, --output=OUTPUT
                        output graph [default: <INPUT>]
  -t TRANSFO, --transformation=TRANSFO
                        transformation file. Transformations may correspond to
                        ROIs, using -n options
  -n NAME, --name=NAME  ROI name to apply transformation to. Any -n option
                        must correspond to a -t option. If no -n option is
                        specified, a global, single -t transformation may be
                        applied.

cartoLinearComb.py

Usage: cartoLinearComb.py [options]

Apply a formula to a set of homogeneous images or textures (homogeneous means
all of the same data type)

Options:
  -h, --help            show this help message and exit
  -o OUTPUT, --output=OUTPUT
                        output volume
  -f FORMULA, --formula=FORMULA
                        image formula, ex: ( I1 * 2 + I2 * I3 ) / 1.2
  -i FILENAME, --input=FILENAME
                        input volume(s)

cartoSetMinf.py

Usage: cartoSetMinf.py [options]

set/create properties in a .minf header

Options:
  -h, --help            show this help message and exit
  -i INPUT, --inpput=INPUT
                        input .minf
  -p PROPERTY, --property=PROPERTY
                        property to set
  -v VALUE, --value=VALUE
                        property value (12, or "toto", or [ 1.2, 12 ]. Be
                        careful to put two quotes around numeric expressions
                        that are meant to be strings (one quote for the shell,
                        one for pyhton: "'12.5'") otherwise they will be taken
                        as numbers. Multiple property/value pairs are allowed
                        but must have matching numbers
  -e EXPRESSION, --expression=EXPRESSION
                        expression to apply, ex: attributes.update( { "toto" :
                        12, "tutu" : [ 1.2, 12.5 ] } , or del attributes[
                        "toto" ]

meshCleaner

(Compiled at 10:16:07 on Sep 11 2018)
Reading mesh...
    meshCleaner
    -----------

removingPointsWithHighCurvature

Options :

-i <file name (read only): Mesh of VOID>
    input mesh

-o <filename: Mesh of VOID>
    output mesh

-maxCurv <FLOAT>
    maximum unoriented Gaussian curvature allowed in the mesh

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


anatomist

Starting Anatomist.....

    anatomist
    ---------

Anatomist GUI

Options :

[ -i | --input <vector of string> ]
    loads these files (conataining either Anatomist/AIMS objects, or .ana
    commands files)

[ -p | --pipe <vector of string> ]
    open named pipe to read commands from (differs from normal .ana files
    loading in that the pipe is not closed once read, the pipe is reopened once
    flushed - using -p for a regular file results in infinite rereading of the
    same commands file)

[ -b | --batch <boolean> ]
    batch mode: no control window (for remote control only, normally used with
    -p or a .ana input)

[ -s | --server <S32> ]
    server mode: anatomist will listen on the given TCP port for command stream
    connections

[ -u | --userprofile <string> ]
    user profile: all personal data will use the directory
    <home_dir>/.anatomist-<userprofile> rather than the default
    <home_dir>/.anatomist

[ --userLevel <S32> ]
    sets the user level: 0: basic, 1: advanced, 2: expert, >=3: debugger
    (enables unstable features which may make Anatomist badly crash)

[ --cout <string> ]
    redirect outpout messages to a file

[ --cerr <string> ]
    redirect error messages to a file

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)

Exiting Anatomist --- Goodbye.
Palette Blue-Red not found.
AObjectPalette::set : warning: palette "toto" not found

mkhierarchy-anatomist

usage : bin/mkhierarchy-anatomist inputfile outputfile
inputfile  : .roi_names_template ou un fichier de même format
outputfile : fichier arbre de hierarchie AnaQt (.hie)

anaAtlasViewer.py

Usage: Atlas viewer and ROIs selector

Options:
  -h, --help            show this help message and exit
  -i FILE, --input=FILE
                        input model/atlas graph[s] (.arg). Selveral items
                        allowed.
  -v FILE, --volume=FILE
                        volume which may be viewed optionally
  -s FILE, --sel=FILE   selection file for pre-selected regions/groups
  -n FILE, --nomenclature=FILE
                        nomenclature file (.hie) for names and colors

anaSulciSnapshot.py

Starting Anatomist.....
config file : /home/dr144257/.anatomist/config/settings.cfg
PyAnatomist Module present
global modules: /volatile/riviere/brainvisa/build-stable-qt5/share/anatomist-4.6/python_plugins
home   modules: /home/dr144257/.anatomist/python_plugins
loading module selection
loading module profilewindow
loading module gradientpalette
loading module bundles_split_by_cortical_regions
loading module volumepalettes
loading module histogram
loading module foldsplit
loading module bundles_small_brains
loading module modelGraphs
loading module bsa_proba
loading module meshsplit
loading module palettecontrols
loading module paletteViewer
loading module anacontrolmenu
loading module synccameracontrol
all python modules loaded
Anatomist started.
Usage: Snapshots...
--mesh is optional.

Options:
  -h, --help            show this help message and exit
  --orientation=TYPE    one of left, right, top, bottom (default : left)
  -g FILE, --graph=FILE
                        graph of sulci
  -m FILE, --mesh=FILE  mesh : grey/white
  -t FILE, --transformation=FILE
                        trm file : subject -> Talairach, default: take it from
                        graph
  -o FILE, --outimage=FILE
                        output image name
  -s NAME, --sulci=NAME
                        Select and display only specified sulci (coma-
                        separated list)
  -q VALUES, --quaternion=VALUES
                        Set orientation of camera by hand from anatomist
                        quaternion (see history.ana). 4 floatting values
                        splitted by commas. ex: 1,2,3,4
  -b VALUES/FILE, --bounding-box=VALUES/FILE
                        Set bounding box of camera (default: autofocus).
                        VALUES=6 floatting values splitted by comas and semi-
                        column. ex: 1,2,3;4,5,6 FILE=list of bounding box, one
                        per line. ex: ([1, 2, 3], [4, 5, 6])
  -f FILE, --bounding-box-file=FILE
                        Append boundingbox to this file (one per line)
  --nodisplay           no display.
  --label-mode=FILE     use 'label' or 'name' attribute to display sulci
                        (default : name)
  --translation=FILE    translation file (default :
                        /volatile/riviere/brainvisa/build-stable-qt5/share
                        /brainvisa-share-4.6/nomenclature/translation/sulci_mo
                        del_noroots.trl)
  --hie=FILE            hiearchy (default : /volatile/riviere/brainvisa/build-
                        stable-qt5/share/brainvisa-share-4.6/nomenclature/hier
                        archy/sulcal_root_colors.hie)
  --size=VALUES         Size (width,height) of the snapshot. 2 int values
                        separated by a coma. ex: 1024,768, 0,0: fullscreen
                        (default)

anasimpleviewer.py

Usage: anasimpleviewer.py [options]

A simplified version of Anatomist for quick viewing

Options:
  -h, --help            show this help message and exit
  -i FILE, --input=FILE
                        load given objects from files
  -l, --left            Use left button for rotation in 3D view

autocrop.py

bin/autocrop.py input output

mosaic.py

Usage: Mosaic...
Usage: mosaic.py -o output -n n     [-r] img1.png img2.png...       mosaic.py -o output -s n1xn2 [-r] img1.png img2.png...

Options:
  -h, --help            show this help message and exit
  -o FILE, --output=FILE
                        output filename. If several files are created there
                        will be named file_N.ext with the given file.ext
                        parameter and N a  variable number for each output.
  -n INT, --number=INT  number of pages
  -s INTxINT, --shape=INTxINT
                        number of rows x columns example: 3x2 (default:
                        disable)
  -r FLOAT, --ratio=FLOAT
                        page ratio (default : 4./3 landscape)

axon-runprocess

Usage: axon-runprocess [options] processname [arg1] [arg2] ... [argx=valuex] [argy=valuey] ...

Example:
axon-runprocess --enabledb threshold ~/data/irm.ima /tmp/th.nii threshold1=80

Named arguments (in the shape argx=valuex) may address sub-processes of a pipeline, using the dot separator:

PrepareSubject.t1mri=/home/myself/mymri.nii

For a more precise description, please look at the web documentation:
http://brainvisa.info/axon/user_doc/axon_manual2.html#brainvisa-commandline


Run a single BrainVISA / Axon process

Options:
  -h, --help            show this help message and exit

  Config:
    Processing configuration, database options

    --enabledb          enable databasing (slower startup, but all features
                        enabled)
    --historyBook=HISTORYBOOK
                        store history information files in this directory
                        (otherwise disabled unless dabasing is enabled)
    --logFile=LOGFILE   specify the log file to use. Default is the usual
                        brainvisa.log if databasing is enabled, else no log
                        file is used.

  Processing:
    Processing options, distributed execution

    --swf, --soma_workflow
                        use soma_workflow. Soma-Workflow configuration has to
                        be setup and valid for non-local execution, and
                        additional login and file transfer options may be used
    -r RESOURCE_ID, --resource_id=RESOURCE_ID
                        soma-workflow resource ID, defaults to localhost
    -u LOGIN, --user=LOGIN
                        login to use on the remote computing resource
    -p PASSWORD, --password=PASSWORD
                        password to access the remote computing resource. Do
                        not specify it if using a ssh key
    --rsa-pass=RSA_KEY_PASS
                        RSA key password, for ssh key access
    --queue=QUEUE       Queue to use on the computing resource. If not
                        specified, use the default queue.
    --input-processing=INPUT_FILE_PROCESSING
                        Input files processing: local_path, transfer,
                        translate, or translate_shared. The default is
                        local_path if the computing resource is the localhost,
                        or translate_shared otherwise.
    --output-processing=OUTPUT_FILE_PROCESSING
                        Output files processing: local_path, transfer, or
                        translate. The default is local_path.
    --keep-workflow     keep the workflow in the computing resource database
                        after execution. By default it is removed.
    --keep-failed-workflow
                        keep the workflow in the computing resource database
                        after execution, if it has failed. By default it is
                        removed.

  Iteration:
    Iteration

    -i ITERATE_ON, --iterate=ITERATE_ON
                        Iterate the given process, iterating over the given
                        parameter(s). Multiple parameters may be iterated
                        joinly using several -i options. In the process
                        parameters, values are replaced by lists, all iterated
                        lists should have the same size. Ex: axon-runprocess
                        -i par_a -i par_c a_process par_a="[1, 2]"
                        par_b="something" par_c="[\"one\", \"two\"]"

  Help:
    Help and documentation options

    --list-processes    List processes and exit. sorting / filtering are
                        controlled by the following options.
    --sort-by=SORT_BY   List processed by: id, name, toolbox, or role
    --proc-filter=PROC_FILTER
                        filter processes list. Several filters may be used to
                        setup several rules. Rules have the shape:
                        attribute="filter_expr", filter_expr is a regex. Ex:
                        id=".*[Ss]ulci.*"
    --hide-proc-attrib=HIDE_PROC_ATTRIB
                        in processes list, hide selected attribute (several
                        values allowed)
    --process-help=PROCESS_HELP
                        display specified process help

brainvisa

  File "bin/brainvisa", line 13
    nosymlink='
              ^
SyntaxError: EOL while scanning string literal

VipAlternatedSequentialFilter


------------------------------
VIP Info:
	 Succession of opening and closing on an object defined as all non zero points
------------------------------
The structuring element is a ball of radius size for a chamfer distance.

Usage: VipAlternatedSequentialFilter
		-i[nput] {image name} : object definition
		[-s[ize] {maximum opening size in mm (default:1 mm)}]
		[-S[ize] {maximum closing size in mm (default:same as opening size)}]
The maximum size corresponds to the last cycle structure element size.
For each iteration, the structure element size is Iter*SizeMax/Ncycle
		[-N[cycle] number of cycle {int (default:1)}]
		[-f[irst] {char: o or c (default:"o")}]
o:opening first,  c:closing first
		[-a[lgo] {char: f or t (default:"f")}]
f:bounded thick front propagation, t: chamfer transformation
		[-n[itermax] {int (default:5)}]
maximum number of iterations for Voronoi iterated chamfer transform
		[-o[utput] {image name (default:"smoothed")}]
		[-x[masksize] {int (default:3)}: chamfer mask xsize]
		[-y[masksize] {int (default:3)}: chamfer mask ysize]
		[-z[masksize] {int (default:3)}: chamfer mask zsize]
		[-m[ultfactor] {float (default:VIP_USUAL_DISTMAP_MULTFACT)}]
		[-c[onnectivity] {string:n/6/18/26/4/8/4s/8s/4c/8c (default:6)}]
"n" means not used. Suffixes "s" and "c" means sagittal and coronal orientations
		[-r[eadformat] {char: v, s or t (default:v)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
		[-w[riteformat] {char: v, s or t (default:v)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
		[-h[elp]

VipAngleToDeplacement


------------------------------
VIP Info:
	 Creates a deplacement files from translation and rotation angles
------------------------------

Usage: VipAngleToDeplacement
		-o[utput] {file name}
		[-x[trans] X translation in mm {float (default:0.0)}]
		[-y[trans] Y translation in mm {float (default:0.0)}]
		[-z[trans] Z translation in mm {float (default:0.0)}]
		[-a[lpha] rotation around X in degree {float (default:0.0)}]
		[-b[eta] rotation around Y in degree {float (default:0.0)}]
		[-g[amma] rotation around Z in degree {float (default:0.0)}]
		[-X[center] X rotation center position in mm {float (default:0.0)}]
		[-Y[center] Y rotation center position in mm {float (default:0.0)}]
		[-Z[center] Z rotation center position in mm {float (default:0.0)}]
		[-h[elp]

VipBiasCorrection


------------------------------
VIP Info:
	 Computes a smooth multiplicative field which corrects for non stationarities.

------------------------------
This field aims at minimizing the volume entropy (= minimizing information...).
A tradeoff is found between this entropy and the internal energy of a membrane using annealing.

Usage: VipBiasCorrection
        -i[nput] {image name}
        [-o[utput] {image name (default:"nobias")}]
        [-f[ield] {bias field name (default:"field")}]
        [-D[imfield] {type of field (2/3) (default:3)}]
2: the correction field is constant by slice, 3: constant by cubes
        [-F[write] {write field: y/n (default:y)}]
        [-d[umb] {y/n (default:y)}]
        [-Ke[ntropy] {float  (default:1.)}]
Weight of the volume entropy which will be multiplied by the field size
        [-Kr[egul] {float  (default:20.)}]
Weight of the membrane/spline energy (sum of the squared log of the ratio between 6-neighbors)
        [-Ko[ffset] {float  (default:0.5)}]
Weight of the squared difference between old and new mean
        [-c[ompression] {int [0,14]  (default:auto)}]
The number of bits which are discarted during the volume entropy computation (= /2^compression))
        [-tl[ow] {int (default:3*2^compression)}]
        [-th[igh] {int (default:not used)}]
        [-e[ges] {int (default:not used, else 2/3)}]
remove 2D/3D edges for histogram estimation (discard partial volume)
        [-vt[ariance] {int (default:not used, else int threshold)}]
high threshold on standard deviation in 26-neighborhood for inclusion in histogram
Values beyond this threshold are not taken into account.
In return, the field correction is applied to all values to get the final result
        [-vp[ourcentage] {int (default:not used, else int threshold)}]
Pourcentage of non null points kept with a ranking stemming from local variance
        [-T[emperature] {float (default:10.)}]
Initial temperature for annealing
        [-G[rid] {int (default:2)}]
Number of grid for minimization (annealing on the highest only)
        [-g[eometric] {float (default:0.97)}]
Geometric decreasing for annealing schedule
        [-s[ampling] {float  (default:16mm)}]
The sampling of the field: one value for a parallelepipedic volume of points.
In each direction, the sampling is: sampling/DirVoxelSize.
The field is a 0-order spline during optimization (piecewise constant)
               3-order spline during the final bias correction (piecewise linear)
        [-n[Increment] {int (default:2)}]
Minimization is performed using a Gibbs sampler or a ICM (deterministic) approach with
several multiplicative increments are tires for each field point:
1/I^n,...,1/I,I,...I^n:
        [-I[ncrement] {float (default:1.03)}]
elementary multiplicative increment (see above):
        [-a[mplitude] {float ]1,10]  (default:1.1)}]
The field random initialization is in the range [1/amplitude, amplitude]
        [-Z[regulTuning] {float  (default:1)}]
Multiplicative factor for regularization in z direction (bad coil)
        [-r[eadformat] {char: a, v, s or t (default:any)}]
        [-w[riteformat] {char: v, s or t (default:t)}]
        [-h[elp]
More information in:
Entropy minimization for automatic correction
of intensity non uniformity, J.-F. Mangin,
MMBIA (Math. Methods in Biomed. Image Analysis),
Hilton Head Island, South Carolina, IEEE Press
162-169, 2000

VipCSFSeg

Usage: VipCSFSeg
        -i[nput] {MR image (bias corrected)}
        -o[utput] {}
        [-r[eadformat] {char: a, v, s or t (default:a)}]
        [-w[riteformat] {char: v, s  or t (default:t)}]
        [-srand {int (default: time}]
        [-h[elp]

VipClosing


------------------------------
VIP Info:
	 Dilates the object defined as all non zero points
------------------------------
The structuring element is a ball of radius size for a chamfer distance.

Usage: VipClosing
        -i[nput] {image name} : object definition
        -s[ize] {closing size in mm.}
        [-a[lgo] {char: f or t (default:"f")}]
f:bounded thick front propagation, t: chamfer transformation
        [-o[utput] {image name (default:"closed")}]
        [-x[masksize] {int (default:3)}: chamfer mask xsize]
        [-y[masksize] {int (default:3)}: chamfer mask ysize]
        [-z[masksize] {int (default:3)}: chamfer mask zsize]
        [-m[ultfactor] {float (default:VIP_USUAL_DISTMAP_MULTFACT)}]
        [-c[onnectivity] {string:6/18/26/4/8/4s/8s/4c/8c (default:26)}]
Suffixes "s" and "c" means sagittal and coronal orientations
        [-r[eadformat] {char: a, v, s or t (default:a)}]
a = any
        [-w[riteformat] {char: v, s or t (default:t)}]
        [-h[elp]

VipClusterArg


------------------------------
VIP Info:
	 Create a SPM cluster based attributed relational graph
------------------------------

Example: VipClusterArg -i circuit_attention -s 5
Then load circuit_attention.arg in Anatomist
and put it in 2D and 3D visualization windows
Warning: put a normalized anatomical image in 2D window before clusters
Manipulate using a browser or a dedicated hierarchy

        -i[nput] {image name}
You can get it from SPM during in the RESULT section from the WRITE button

        [-t[ransfo] {3D rotation/translation (default:none)}
If you are not satisfied with the link between the contrast image
and the anatomical image that is computed from SPM center
you can provide your own translation (perhaps modifying
slightly the printed one...)
The transfo file format is the following:
tx ty tz
1. 0. 0.
0. 1. 0.
0. 0. 1.
If you are a wizard, you can even add a rotation matrix...
My advice relative to translation sign:
try first with large translation. Indeed according
to normalized or non normalized situation, image may be variously flipped

        [-n[ormalisation] {ascii file (default:none)}
This flag is used to get Talairach coordinate when playing
with non normalized data.
This file is an ASCII/Anatomist version of SPM anatSXXXX_sn3d.mat
You get it with the command:
AnaImportSPMsn3dFile <SXXXX_002>
        [-T[emplate] {volume (default:/home/Panabase/demo/talairach/nanatRa)}
Usually the T1-weighted anatomical volume on which you will visualize the clusters in 2D
This volume gives image size and resolution
        [-o[utput] {arg name (default:"input")}]
        [-s[ize] {int: min cluster size in 18-connectivity (default:0)}]
        [-m[esh] {char: y/n (default:y)}]
Trigger the mesh generation
With large clusters, this can be very expensive
In most situation, you can work only with voxels
but Anatomist takes some time to yield the first visualization
        [-r[eadformat] {char: v, s or t (default:any)}]
        [-h[elp]

VipConnexFilter


------------------------------
VIP Info:
	 Removes connected component according to their size
------------------------------
the smallest ones can be removed or one of the biggest kept.
It is also possible to get a labelling

Usage: VipConnexFilter
        -i[nput] {image name} : object definition
        [-o[utput] {image name (default:"distmap")}]
        [-d[ual] (work on background)]
        [-s[ize] {int (default:0)} : smaller will be removed]
        [-b[iggest] {int (default:1)} : you can choose first, second...]
        [-m[ode] {b, g or l (default:g)} : binary, grey result or labelling (1,2,3...)]
        [-c[onnectivity] {string:6/18/26/4/8/4s/8s/4c/8c (default:26)}]
Suffixes "s" and "c" means sagittal and coronal orientations

------------------------------
VIP Info:
	 Read and Write flag are actually configured for debugging...
------------------------------
        [-r[eadformat] {char: a, s, v or t (default:any)}]
        [-w[riteformat] {char: s, v or t (default:t)}]
        [-h[elp]

VipConvert


------------------------------
VIP Info:
	 Converts any volume to another type
------------------------------

Usage: VipConvert
        -i[nput] {image name}
        [-t[ype] {U8/S16/F (default:S16)}]
Be aware that the default reading and writing format is vida unscaled (S16BIT)
        [-o[utput] {image name (default:"converted")}]
        [-s[plit] {y/n to create SPM dynamic format (default n)}]
put this flag to s to trigger conversion of a dynamic image to SPM format
        [-m[ode] {r (default:r (raw))}]
with r mode, the conversion is a simple cast
        [-r[eadformat] {char: v, s or t (default: scaled vida)}]
Forces the reading of VIDA, SPM or TIVOLI image file format
By default, the vida scaled reading to float volume is used
When -r v is asked, the vida reading to S16BIT is used
        [-w[riteformat] {char: v, s or t (default: unscaled vida)}]
Forces the writing of VIDA, SPM or TIVOLI image file format
the v choice forces scaled writing of float volume to vida format
the default mode do not scaled the volume
        [-h[elp]
Examples:
-----------------------------------------------------
Conversion d'une image d'index DTI (trace, volume ratio...)
L'image a convertir est au format TIVOLI (ima/dim) en float (verifiez dans le .dim)
-->VipConvert -i trace -o traceSPM -w s -t F
-----------------------------------------------------
Conversion d'une serie dynamique type IRMf pour SPM
L'image a convertir est au format VIDA
-->VipConvert -i raw -o frame -w s -s yn
-----------------------------------------------------

VipCovarianceMatrix


------------------------------
VIP Info:
	 Compute the covariance matrix from a data matrix.
------------------------------
Usage: VipCovarianceMatrix
		-i[nput] {ASCII data file}
		-f[eature] {number of features}
		-p[opulation] {number of individuals in population}
		[-o[utput] {ASCII result file without extension (default:output on stdout)}]
		[-t[type] {n | i (default:n)}]
			d=NORMAL, i=INVERSE
		[-d[iagonal]] {only get the matrix diagonal}
		[-m[ean]] {generates an additional ASCII file of means}
		[-h[elp]]


VipCylinder


------------------------------
VIP Info:
	 Create a triangulated  cylinder given by two extremities
------------------------------
If a template is specified, extremities are specified as coordinates
Otherwise, they are supposed to be in mm

Usage: VipCylinder
        [-t[emplate]] {coordinates in this image }
        [-o[utput] {cylinder name (default:"cylinders")}]
        -x1 {float }
        -x2 {float }
        -y1 {float }
        -y2 {float }
        -z1 {float }
        -z2 {float }
        [-r[adius] {float (default:0.5mm)}]
        [-ha[theight] {float (default:0mm)}]
        [-h[elp]

VipDeriche


------------------------------
VIP Info:
	 Computes gradient using deriche 2D recursive filters
------------------------------
Such filters include optimal smoothing according to Canny criteria.

Usage: VipDeriche
        -i[nput] {image name}
        [-a[lpha] {float (default:1.) (range:[0.3,3]}]
The smoothing importance decreases when alpha increases
        [-o[utput] {image name (default:"deriche")}]
        [-s[ave] {y/n (default:n)}]
save a .g2D file with gradient coordinates for inflation
during surface matching
        [-f[ilter] {e/n/x/y/z/s (default:e (extrema))}]
e: norm extrema in the gradient direction
n: norm
x: x gradient coordinate
y: y gradient coordinate
z: z gradient coordinate
s: smoothing
        [-t[hreshold] {int (default:0)}]
No extremum detection under threshold value
Other images are thresholded according to threshold value
        [-d[im] {2/3 (default:3)}]
        [-r[eadformat] {char: v or t (default:t)}]
        [-w[riteformat] {char: v or t (default:t)}]
        [-h[elp]

VipDilation


------------------------------
VIP Info:
	 Dilates the object defined as all non zero points
------------------------------
The structuring element is a ball of radius size for a chamfer distance.

Usage: VipDilation
        -i[nput] {image name} : object definition
        -s[ize] {dilation size in mm.}
        [-a[lgo] {char: f or t (default:"f")}]
f:bounded thick front propagation, t: chamfer transformation
        [-o[utput] {image name (default:"dilated")}]
        [-x[masksize] {int (default:3)}: chamfer mask xsize]
        [-y[masksize] {int (default:3)}: chamfer mask ysize]
        [-z[masksize] {int (default:3)}: chamfer mask zsize]
        [-m[ultfactor] {float (default:VIP_USUAL_DISTMAP_MULTFACT)}]
        [-c[onnectivity] {string:6/18/26/4/8/4s/8s/4c/8c (default:26)}]
Suffixes "s" and "c" means sagittal and coronal orientations
        [-r[eadformat] {char: a, v, s or t (default:a)}]
a = any
        [-w[riteformat] {char: v, s or t (default:t)}]
        [-h[elp]

VipDistanceMap


------------------------------
VIP Info:
	 Computes a chamfer distance to the object defined as all non zero points
------------------------------
Distances either correspond to Euclidean distance multiplied by multfactor.
or correspond to the distance related to the specified connectivity.

Usage: VipDistanceMap
        -i[nput] {image name} : object definition
        [-o[utput] {image name (default:"distmap")}]
        [-c[onnectivity] {string:6/18/26/4/8/4s/8s/4c/8c (default:not used)}]
        [-g[eodesic] {string:'i' or 'f' (default:not used)}]
geodesic distance map: 'i':iterated chamfer transform
                       'f':thick front propagation
        [-d[omain] {int (default:0)}]
this value defines propagation domain for the geodesic distance
        [-f[orbiden] {int (default:-1)}]
this value defines outside of domain for the geodesic distance
        [-l[imit] {int (default:not used)}]
For front propagation, the propagation is stoped beyond limit (mm or bonds)
        [-lm[ode] {int ('n,'l','f','i') (default:n)}]
according to this mode, the value given to the domain beyond limit is
l:limit*MULT_FACTOR, f: forbidden value, i: infinite (large) value
        [-n[itermax] {int (default:5)}]
maximum number of iterations for iterated chamfer transform
Suffixes "s" and "c" means sagittal and coronal orientations
        [-x[masksize] {int (default:3)}: chamfer mask xsize]
        [-y[masksize] {int (default:3)}: chamfer mask ysize]
        [-z[masksize] {int (default:3)}: chamfer mask zsize]
        [-m[ultfactor] {float (default:50)}]
        [-r[eadformat] {char: a, v, s or t (default:any)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
        [-w[riteformat] {char: v, s or t (default:t)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
        [-h[elp]

VipDoubleThreshold


------------------------------
VIP Info:
	 Applies a double threshold to input image according to << mode >> and << type >>
------------------------------

Usage: VipDoubleThreshold
        -i[nput] {image name}
        -tl {int (low threshold)
        -th {int (high threshold)
        [-fl] {float (low threshold)}
        [-fh] {float (high threshold)}
If fl and fh are given, tl and th are no more required...
        [-o[utput] {image name (default:"thresholded")}]
        [-m[ode] {b | be | o | oe (default:be)}]
b=BETWEEN, be=BETWEEN_OR_EQUAL_TO, o=OUTSIDE, oe=OUTSIDE_OR_EQUAL_TO
        [-c[olor] {b | g (default:g)}]
Output image nature: b=BINARY_RESULT: ( 255 / 0 ), g=GREYLEVEL_RESULT
        [-r[eadformat] {char: a, v, s or t (default:any)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
        [-w[riteformat] {char: v, s or t (default:t)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
        [-h[elp]

VipEpiCorrect

Syntax : 
epi_correct [parameter_file] distorted_epi corrected_epi phasemap 
phasemap : an error occured ; exiting... 

VipEpiDistParam

parameter file : 
------------------------------
VIP Info:
	 Fill in parameter file required by VipEpiCorrect
------------------------------

Usage: VipEpiDistParam
        param filename (interactive mode)
        -b[atch] {command line mode} with the following options:
          [-dex {double echo image - size x (default 128)}]
          [-dey {double echo image - size y (default 128)}]
          [-dez {double echo image - size z (default 128)}]
          [-epix {epi image - size x  (default 64)}]
          [-epiy {double echo image - size z (default 64)}]
          [-epit {epi image - number of repetitions (default 22)}]
          [-revz {epi - reverse z axis ? (y/n) (default y)}]
          [-iet {inter_echo_time in ms: delay between successive echos (default 2.28)}]
          [-dwt {dwell_time in ms: delay between successive echos in EPI image (default 0.64)}]
        [-h[elp]
Example:
-----------------------------------------------------
Mode interactif: le répertoire courant contient fidNN.raw au format Brucker
-->VipEpiDistParam distparam.txt
-----------------------------------------------------
Mode batch
Mode batch: le répertoire courant contient fidNN.raw au format Brucker
Choix par défaut pour tous les paramètres: 
-->VipEpiDistParam distparam.txt -b 
Autres choix pour les paramètres dex dey dez epix epiy epit revz
VipEpiDistParam distparam.txt -b -dex 256 -dey 256 -dez 256 -epix 128 -epiy 128 -epit 30 -revz n 
-----------------------------------------------------

VipEpiPhaseMap

Syntax : 
phasemap [parameter_file] raw_grad_echo output_phasemap distorted_epi 
an error occured reading the parameters; exiting... 

VipErosion


------------------------------
VIP Info:
	 Erodes the object defined as all non zero points
------------------------------
The structuring element is a ball of radius size for a chamfer distance.

Usage: VipErosion
        -i[nput] {image name} : object definition
        -s[ize] {erosion size in mm.}
        [-a[lgo] {char: f or t (default:"f")}]
f:bounded thick front propagation, t: chamfer transformation
        [-o[utput] {image name (default:"eroded")}]
        [-x[masksize] {int (default:3)}: chamfer mask xsize]
        [-y[masksize] {int (default:3)}: chamfer mask ysize]
        [-z[masksize] {int (default:3)}: chamfer mask zsize]
        [-m[ultfactor] {float (default:VIP_USUAL_DISTMAP_MULTFACT)}]
        [-c[onnectivity] {string:6/18/26/4/8/4s/8s/4c/8c (default:26)}]
Suffixes "s" and "c" means sagittal and coronal orientations
        [-r[eadformat] {char: v or t (default:v)}]
        [-w[riteformat] {char: v or t (default:v)}]
        [-h[elp]

VipExtEdge


------------------------------
VIP Info:
	 Returns edges touched by rays casted from image borders
------------------------------
Then removes connected component according to their size
the smallest ones can be removed or one of the biggest kept.

Usage: VipExtEdge
        -i[nput] {image name} : object definition
        [-o[utput] {image name (default:"extedge")}]
        [-m[ode] {3Da/3D-ztop/3D-zbot/2Da/2D-ytop/2D-ybot (default:2Da)}]
Just a way of specifying borders...
        [-f[ill] {y/n (default:n)}]
        [-g[radient] (2/3 (default:not used)]
        [-s[ize] {int (default:0)} : smaller will be removed]
        [-b[iggest] {int (default:1)} : you can choose first, second...]
        [-c[onnectivity] {string:6/18/26/4/8/4s/8s/4c/8c (default:26)}]
Suffixes "s" and "c" means sagittal and coronal orientations
        [-r[eadformat] {char: v, s or t (default:t)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
        [-w[riteformat] {char: v, s or t (default:t)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
        [-h[elp]

VipFileDump


------------------------------
VIP Info:
	 Binary file dump.
------------------------------

Usage: VipDumpFile
		-i[nput] {binary file name}
		[-h[elp]]

For large file, use: VipDumpFile -i binaryFile | more

VipFlip


------------------------------
VIP Info:
	 Flips volume either in a miror way or swaping coordinates
------------------------------

Usage: VipFlip
        -i[nput] {image name}
        -m[ode] {xx,yy,zz,xy,xz,yz,xxzz,yyzz}
        [-o[utput] {image name (default:"flipped")}]
with r mode, the conversion is a simple cast
        [-r[eadformat] {char: v, s or t (default: scaled vida)}]
Forces the reading of VIDA or TIVOLI image file format
By default, the vida scaled reading to float volume is used
When -r v is asked, the vida reading to S16BIT is used
        [-w[riteformat] {char: v, s or t (default: unscaled vida)}]
Forces the writing of VIDA, TIVOLI or SPM image file format
the v choice forces scaled writing of float volume to vida format
the default mode do not scaled the volume
        [-h[elp]

VipFoetusHomotopicSnake

Usage: VipHomotopicSnake
        -i[nput] {segmented brain image name}
        -h[ana] {histogram scale-space analysis (?.han)}]
        [-o[utput] {image name (default:"cortex")}]
        [-fc[losing] {float (mm) closing size for f mode (default: 5)}]
        [-li[nside] {int:label<290 (default:0)}]
        [-lo[utside] {int:label<290 (default:11)}]
        [-p[ressure] {int [0:100] (default:0)}]
        [-mg[ray] {float (default:?.ana)}]
        [-sg[ray] {float (default:?.ana)}]
        [-mw[hite] {float (default:?.ana)}]
        [-sw[hite] {float (default:?.ana)}]
        [-r[eadformat] {char: v or t (default:v)}]
        [-w[riteformat] {char: v or t (default:t)}]
        [-h[elp]

VipFoldArg


------------------------------
VIP Info:
	 Create a fold based attributed relational graph
------------------------------

Usage: VipFoldArg
        -i[nput] {image name} : depends on the algorithm
        [-o[utput] {arg name (default:"someone")}]
        [-a[rg] {arg name for conversion}]
        [-v[oronoi] {roots voronoi image name}]
This voronoi stem from VipSkeleton and represent watershed catchment bassins
of sulcal roots. It is used to split topologically simple surfaces
if this image name is not given, such split will not occur...
        [-s[ize] {int: min ss size (default:15)}]
ss size coorresponds to (ss points + edge points)
        [-li[nside] {int:label<290 (default:0)}]
        [-lo[utside] {int:label<290 (default:11)}]
        [-r[eadformat] {char: v or t (default:v)}]
        [-w[riteformat] {char: o or g (default:o)}]
o: old Arg format
g: Generic Arg format (C++ lib)
        [-h[elp]

VipFoldArgAtt


------------------------------
VIP Info:
	 Computes various Fold Arg semantic attributes (depth,normal...)
------------------------------

Usage: VipFoldArgAtt
        -i[nput] {skeleton name}
        -a[rg] {fold arg name}
        [-o[utput] {arg name (default:"input arg name")}]
        [-li[nside] {int:label<290 (default:0)}]
        [-lo[utside] {int:label<290 (default:11)}]
        [-T[alairach] {y/n (default:y)}]
        [-t[riangulation] {char:yes/no/only (default:n)}]
        [-lh[emi] {left hemisphere image name}]
        [-rh[emi] {right hemisphere image name}]
        [-P[oints] {AC,PC,IH coord filename (*.tal) (default:not used)}]
Correct format for the commissure coordinate file toto.APC:
AC: 91 88 113
PC: 91 115 109
IH: 90 109 53
        [-xA[C] {(int [0-xsize[) AC X coordinate}]
        [-yA[C] {(int [0-ysize[) AC Y coordinate}]
        [-zA[C] {(int [0-zsize[) AC Z coordinate}]
        [-xP[C] {(int [0-xsize[) PC X coordinate}]
        [-yP[C] {(int [0-ysize[) PC Y coordinate}]
        [-zP[C] {(int [0-zsize[) PC Z coordinate}]
        [-xI[nterHem] {(int [0-xsize[) Inter-hemis. point X coord.}]
        [-yI[nterHem] {(int [0-ysize[) Inter-hemis. point Y coord.}]
        [-zI[nterHem] {(int [0-zsize[) Inter-hemis. point Z coord.}]
        [-r[eadformat] {char: v or t (default:v)}]
        [-w[riteformat] {char: o or g (default:o)}]
o: old Arg format
g: Generic Arg format (C++ lib)
        [-h[elp]

VipGaussian


------------------------------
VIP Info:
	 Computes convolution by a 3D gaussian using Deriche recursive filters
------------------------------
Sigma is adapted to the voxel size in each direction

Usage: VipGaussian
        -i[nput] {image name}
        [-s[igma] {float (mm)  (default:largest pixel size)}]
        [-o[utput] {image name (default:"gaussian")}]
        [-f[loat] {y/n (default:n)}]
if n: output keeps the type of input, y: output is in float
        [-r[eadformat] {char: v or t (default:v)}]
        [-w[riteformat] {char: v or t (default:v)}]
        [-h[elp]

VipGeometry


------------------------------
VIP Info:
	 Computes a differential invariant
------------------------------
For the Gaussian filtering Sigma is adapted to the voxel size in each direction
The result is a float Tivoli/GIS format

Usage: VipGeometry
        -i[nput] {image name}
        [-m[ode] {mc/gc/mlvv/glvv/pc1/pc2  (default:mc)}]
mc = isophote mean curvature, gc=isophote Gaussian curvature
mlvv = isophote mean Lvv, gc=isophote Gaussian Lvv
mc = isophote principal curvature 1, gc=isophote principal curvature 2 (pc1>pc2)
la = Laplacian, nla = Normalized Laplacian
        [-s[igma] {float (mm)  (default:largest pixel size)}]
Apply a smoothing (scale=sigma*sigma) to compute differentials in scale-space
        [-g[aussian] {y/n (default:y)}]
        [-H[isto2D] {y/n (default:n)}]
        [-G[radient] {y/n (default:n)}]
        [-M[asked] {image name for Histo2D (default:"input")}]
        [-T[hreshold] {on masked image for Histo2D (default:"1")}]
        [-G[inf] {float   (min of geometry for Histo2D (default: -10))}]
        [-G[sup] {float   (max of geometry for Histo2D (default: 10))}]
        [-o[utput] {image name (default:"geometry")}]
        [-r[eadformat] {char: v or t (default:v)}]
        [-h[elp]

VipGetBrain


------------------------------
VIP Info:
	 Performs brain segmentation using T1-histogram scale space analysis and morphomath
------------------------------
Note that the goal is to get a mask of the brain to further segment hemispheresTherefore, the cerebellum may be eroded or connected to some other tissues,You may get rid of that problem with some non default values, I hope...
Usage: VipGetBrain
        -i[nput] {image name}
        [-b[rain] {char y/n: write segmented brain, default:y}]
        [-bn[ame] {brain image name, default:brain_input}]
        [-R[idge] {White ridge image name (default: not used)}]
        [-V[ariance] {Variance image name (default: not used)}]
        [-E[dges] {Edges image name (default: not used)}]
        [-m[ode] {char: V[2010], 5[2005], S[tandard], R[obust], s[tandard], r[obust], f[ast], default:S}]
Standard: iterative approach to choose best erosion size...
standard: fixed erosion size...
Robust: try to deal with meninge, sinus, Gibbs effect + iterative erosion...
robust: try to deal with meninge, sinus, Gibbs effect + fixed erosion size...
fast: erosion/dilatation...
        [-pa[tho] {pathology binary mask, default:no}]
add a mask of the lesion to be taken into account
This can solve bad morphological process
        [-pm[ode] {char e/i: choice between exclude or include the mask of a lesion in the brain mask, default:e}]
        [-n[iter] {int nb iteration of classif. regularization (def:1)}]
The binary classification is regularized using Markov random field and
ICM minimization (nb iter). This maily prevents the opening effect
of small cavities
fast: two thresholds, erosion, largest cc, dilation
normal: classification + regularisation, erosion, largest cc, dilation + recovering
patho: classification + regularisation, white matter segmentation, whole brain segm.
       this mode is dedicated to pathologies leading to high signal inside the brain
        [-c[olor] {char b/g: binary/graylevel, default:b}]
        [-L[ast] {int (default:3)}]
        [-F[irst] {int (default:1)}]
put Last last slices to zero and First first slices to zero
The aim is to get rid of MR ghost effect disturbing morphomath
BE carefull, the default is related to SHFJ ordering (the neck is in last slices)
WARNING: if your image is spm normalized, put this setting to zero!!!
        [-l[ayer] {int nb of extension into partial volume (def:0, max 2)}]
Add layers of voxels (6-neighbors) if it is improving contrast at mask contour
        [-lo[nly] {char y/n default:n, with yes do only layer processing (reading mask)]
This is for postprocessing of bad quality mask images
        [-f[ill] {char y/n: fill white cavities ,default:y}]
fill in 6-connected cavities of mask which are mainly above white matter mean
        [-C[lose] {char y/n: close the brain , default:n}]
if the 'g' color mode is active, the closing adds gray level 1
        [-C[size] {float: closing size , default:10mm}]
        [-Cn[ame] {closed brain image name, default:closed_input}]
        [-de[bug] {char y/n: debug mode, default:n}]
Write some images, WARNING: the white matter image should not be used as segmentation
    indeed, it is overregularised for robustness of the morphological processing
        [-be[rosion] {float: brain erosion size (default:2.mm)}]
It should be noted that erosion size is dedicated to standard use of the best mode}]
With the other procedures, you may have to increase it a bit to get more robustness,}]
It should also be noted that with a lower erosion size, you could improve}]
the final result with atrophic brains but with a lower robustness relatively to the whole process}]
        [-bd[ilation] {float: brain dilation size (fast mode) (default:be+0.5mm)}]
        [-br[ecover] {float: brain recovering size (default:3.mm)}]
dilation of size (erosion+recover) followed by erosion of size (recover)
        [-we[rosion] {float: white matter erosion size (default:2.1mm)}]
        [-wr[ecover] {float: white matter  recovering size (default:30.mm)}]
dilation of size (erosion+recover) followed by erosion of size (recover)
This parameter are stranges because they are dedicated to the robust approach
where a failure like taking extra white matter tissue) is not problematic
while missing some white matter may be more problematic (but not catastrophic)
        [-a[nalyse] {char y/n/r: automatic histogram analysis, default:y}]
y: automatic, r: read input.his, n: use -gm,-gs,-wm,-ws
        [-hn[ame] {histo analysis, default:input )}]
read when -a r is set, this file has the .han extension (VipHistoAnalysis)
        [-gm[ean] {int : gray matter mean (default:automatic)}]
        [-gs[igma] {int : gray matter standard deviation (default:automatic)}]
        [-wm[ean] {int : white matter mean (default:automatic)}]
        [-ws[igma] {int : white matter standard deviation (default:automatic)}]
        [-Tl[ow] {int : low threshold (default:automatic)}]
        [-Th[igh] {int : high threshold (default:automatic)}]
For fast segmentation, brain tissues = ]Tlow,Thigh[ range
        [-d[scale] {float: (default:0.5)}]
Scale discretization (0.5 is the maximum step for stability)
        [-t[rack] {int (default:5)}]
Track singularities reaching at least this scale
        [-s[tat] {char y/n: write old input.stat file (default:'n')}]
This file is used by an old topologically deformable model stuff
dedicated to g/w interface detection, it should not be used by somebody else...
simple Talairach normalisation may be used to improve sinus deletion
        [-P[oints] {AC,PC,IH coord filename (*.tal) (default:not used)}]
Correct format for the commissure coordinate file toto.APC:
AC: 91 88 113
PC: 91 115 109
IH: 90 109 53
        [-xA[C] {(int [0-xsize[) AC X coordinate}]
        [-yA[C] {(int [0-ysize[) AC Y coordinate}]
        [-zA[C] {(int [0-zsize[) AC Z coordinate}]
        [-xP[C] {(int [0-xsize[) PC X coordinate}]
        [-yP[C] {(int [0-ysize[) PC Y coordinate}]
        [-zP[C] {(int [0-zsize[) PC Z coordinate}]
        [-xI[nterHem] {(int [0-xsize[) Inter-hemis. point X coord.}]
        [-yI[nterHem] {(int [0-ysize[) Inter-hemis. point Y coord.}]
        [-zI[nterHem] {(int [0-zsize[) Inter-hemis. point Z coord.}]
        [-r[eadformat] {char: a, v, s or t (default:any)}]
Forces the reading of VIDA, SPM, TIVOLI or ANY image file format
        [-w[riteformat] {char: v, s or t (default:t)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
        [-h[elp]
More information in:
Robust brain segmentation using histogram
scale-space analysis and mathematical morphology
J.-F. Mangin, O. Coulon, and V. Frouin
MICCAI, MIT, LNCS-1496, Springer Verlag
1230-1241, 1998

VipGetHead

Usage: VipGetHead
        -i[nput] {MRI image name}
        [-h[orn]] {image to be removed}
        [-t[hreshold] {algo t: int (default : not used)}]
        [-o[utput] {image name (default:"head")}]
        [-c[losing] {float (mm) closing size for f mode (default: 4)}]
        [-n[guillotine] {int (default : 3)}]
        [-hn[ame] {histo analysis, default:input )}]
        [-r[eadformat] {char: v or t (default:v)}]
        [-w[riteformat] {char: v or t (default:v)}]
        [-he[lp]
read when -a r is set, this file has the .han extension (VipHistoAnalysis)

VipGetSlice


------------------------------
VIP Info:
	 Extract a slice from a volume
------------------------------
Usage: VipGetSlice
		-i[nput] {image name}
		-s[lice] {slice to extract}
		[-o[utput] {image name (default:"slice")}]
		[-t[ype] {a | c | s (default:a)}]
			a=AXIAL, c=CORONAL, s=SAGITTAL
		[-r[eadformat] {char: v or t (default:v)}]
		[-w[riteformat] {char: v or t (default:v)}]
			v=VIDA, t=TIVOLI
		[-h[elp]]


VipGreyStatFromClassif


------------------------------
VIP Info:
	 Create grey/white statistics file from classif or input

------------------------------
Can be used in case of failure of VipHistoAnalysis because of low grey/white contrast
If you gave a classified or partly classified image, for instance a drawn slice, or the result of
a classification algorithm based on Talairach grid in one way or another
Usage: VipGreyStatFromClassif
        -i[nput] {MR image (bias corrected)}
        -c[lassif] {label image}
        -a[na] {histogram analysis (default input)}]
        [-g[label] {int (default:2)}]
        [-w[label] {int (default:3)}]
        [-mg[ray] {float (default:from classif)}]
        [-sg[ray] {float (default:from classif)}]
        [-mw[hite] {float (default:from classif)}]
        [-sw[hite] {float (default:from classif)}]
        [-r[eadformat] {char: a, v, s or t (default:a)}]
        [-h[elp]

VipGreyWhiteClassif

Usage: VipGreyWhiteClassif
        -i[nput] {MR image (bias corrected)}
        -a[lgo] {char: R[egularisation], N[eighbourhood], default: N}
        -m[ask] {mask or Voronoi diagram}
        -h[ana] {histogram scale-space analysis (?.han)}
        -ed[ges] {edges image name}
        -P[oints] {AC,PC,IH coord filename (*.tal)}
        -ex[ttogrey] {y/n default:y}
        [-l[abel] {int (default:255)}]
        [-n[iterations] {int (default:5)}]
        [-K[Potts] {float (default:20.)}]
        [-c[onnectivity] {string:6/18/26/4/8/4s/8s/4c/8c (default:26)}]
        [-o[utput] {classif (default:"input_greywhite")}]
        [-mg[ray] {float (default:?.han)}]
        [-sg[ray] {float (default:?.han)}]
        [-mw[hite] {float (default:?.han)}]
        [-sw[hite] {float (default:?.han)}]
        [-pa[tho] {pathology binary mask, default:no}]
        [-pm[ode] {char e/w/g: exclude/include as wm/include as gm, default:e}]
        [-r[eadformat] {char: a, v, s or t (default:a)}]
        [-w[riteformat] {char: v, s  or t (default:t)}]
        [-srand {int (default: time}]
        [-he[lp]

VipHistoAnalysis


------------------------------
VIP Info:
	 Performs T1-histogram scale space analysis
------------------------------
        [-o[utput] {histo analysis name (default input))}]
        [-output-his] {histogram name (default output))}]

Usage: VipHistoAnalysis
        -i[nput] {image name/histo name with extension (image.his)}
NB: if the histogram already exists (file name.his or name.his_bin)
it will not be computed again (the volume is not read)analysis will get the han extension
        [-S[AVE] {y/n (default:n)}]
        [-R[idge] {White ridge image name (default: not used)}]
        [-M[ask] {mask to compute histogram (default: not used)}]
Save histogram analysis if performed (Extension: output.han)
        [-m[ode] {char: e[ntropy], v[isu], f[ree], c[ascade], C[ascade], a[nalyse], m[axima], i[teration], default:v}
e: computes some kind of entropy...
v: visu mode send histogram to gnuplot or matplotlib (see -g and --matplotlib options)
h: just writes the histogram
c: cascade mode detects D1/D2 n largest cascades
C: cascade mode detects D1/D2 n highest cascades
a: analyse mode according to contrast
i: iteration of the undersampling factor
s: surface
        [-e[ges] {int (default:not used, else 2/3)}]
remove 2D/3D edges for histogram estimation (discard partial volume)
        [-vt[ariance] {int (default:not used, else int threshold)}]
high threshold on standard deviation in 26-neighborhood for inclusion in histogram
Values beyond this threshold are not taken into account.
        [-vp[ourcentage] {int (default:not used, else int threshold)}]
Pourcentage of non null points kept with a ranking stemming from local variance
        [-u[ndersampling_factor] {int (default:auto)}]
image values are compressed through a division
by undersampling_factor before scale space computation
        [-C[ontrast] {int (default:auto, else h, l or s)}]
h = high, l=low, s= segmented brain, H=Histology, trigger different heuristics for analysis
2 = 2 modes, 3 = 3 modes, 4 = 4 modes 
        [-x[max] {int (default:not used)}]
        [-H[max] {int (default:50000)}]
maxima of axes in the visu mode
        [-d[scale] {float: (default:0.5)}]
Scale discretization (0.5 is the maximum step for stability)
        [-t[rack] {int (default:5)}]
Track singularities reaching at least this scale
        [-O[ffset] {int (default:0)}]
Add an interval of length on the histogram left
        [-s[calemax] {int (default:1000)}]
        [-c[ascade] {int (default:10)}]
        [-0[extrema] {y/n (default:n)}]
        [-1[extrema] {y/n (default:y)}]
        [-2[extrema] {y/n (default:y)}]
        [-3[extrema] {y/n (default:n)}]
        [-4[extrema] {y/n (default:n)}]
        [-g[nuplot] {char: n[o], s[creen], f[ile], p[ostscript], default:n}]
allows you to look at scalespace and histogram using gnuplot
        [--matplotlib {char: n[o], s[creen], f[ile], p[ostscript], default:n}]
same as gnuplot, but uses MatPlotlib instead of GnuPlot
        [-T[itle] {char y/n (default:y)}]
put title in gnuplot drawings
        [-r[eadformat] {char: v, s, t or a (default:a)}]
Forces the reading of VIDA, SPM, TIVOLI(GIS) or ANY image file format
       [-srand {int (default: time}]
Initialization of the random seed, useful to get reproducible results
More information in:
Robust brain segmentation using histogram
scale-space analysis and mathematical morphology
J.-F. Mangin, O. Coulon, and V. Frouin
MICCAI, MIT, LNCS-1496, Springer Verlag
1230-1241, 1998

VipHomotopic

Usage: VipHomotopic
        -i[nput] {MR image (bias corrected)}
        -m[ode] {char: C[ortical interface] or H[emisphere surface]}
        [-o[utput] {image name (default:"cortex")}]
        [-h[ana] {histogram scale-space analysis (?.han) only used by the Cortical mode}]
        [-cl[assif] {grey_white classification image only used by the Cortical mode}]
        [-co[rtex] {cortex image name only used by the Hemisphere mode}]
        [-s[keleton] {skeleton image name only used by the Hemisphere mode}]
        [-v[ersion] {int: 1 or 2 (default: 2)}]
        [-fc[losing] {float (mm) closing size for Cortical mode (default: 10)}]
        [-r[eadformat] {char: v or t (default: v)}]
        [-w[riteformat] {char: v or t (default: t)}]
        [-he[lp]

VipHomotopicSnake

Usage: VipHomotopicSnake
        -i[nput] {segmented brain image name}
        -h[ana] {histogram scale-space analysis (?.han)}]
        [-o[utput] {image name (default:"cortex")}]
        [-fc[losing] {float (mm) closing size for f mode (default: 5)}]
        [-R[idge] {White ridge image name (default: not used)}]
        [-li[nside] {int:label<290 (default:0)}]
        [-lo[utside] {int:label<290 (default:11)}]
        [-p[ressure] {int [0:100] (default:0)}]
        [-mg[ray] {float (default:?.ana)}]
        [-sg[ray] {float (default:?.ana)}]
        [-mw[hite] {float (default:?.ana)}]
        [-sw[hite] {float (default:?.ana)}]
        [-r[eadformat] {char: v or t (default:v)}]
        [-w[riteformat] {char: v or t (default:t)}]
        [-he[lp]

VipHyste


------------------------------
VIP Info:
	 Removes connected component according to their size
------------------------------
the smallest ones can be removed or one of the biggest kept.
It is also possible to get a labelling

Usage: VipHyste
        -i[nput] {image name} : object definition
        -tl {float (low threshold)}
        -th {float (high threshold)}
        [-pl {int in [1..100] (low threshold: percent of max)}]
        [-ph {int in [1..100] (high threshold: percent of max)}]
        [-n[points] {int (default:1) over high threshold}]
        [-q[uotient] {int (quotient=[1..100] points over high threshold)}]
        [-o[utput] {image name (default:"hysteresis")}]
        [-s[ize] {int (default:0)} : smaller will be removed]
        [-g[radient] (2/3 (default:not used)]
read, dwindle ans save .gXD file, where X=2/3
        [-b[iggest] {int (default:1)} : you can choose first, second...]
        [-m[ode] {b, g or l (default:g)} : binary result or labelling (1,2,3...)]
        [-c[onnectivity] {string:6/18/26/4/8/4s/8s/4c/8c (default:26)}]
Suffixes "s" and "c" means sagittal and coronal orientations
        [-r[eadformat] {char: v, s or t (default:v)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
        [-w[riteformat] {char: v, s or t (default:v)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
        [-h[elp]

VipLabelArg


------------------------------
VIP Info:
	 Create a nucleus label based attributed relational graph
------------------------------

        -i[nput] {image name}
        [-m[ode] {n/l (nucleus/label) default:l}]
nucleus mode supposed you use the standard label set
In that case, nucleus names will be given to the VOIs
Hence, you can use nucleus hierarchy in Anatomist
        [-t[riangulation] {y/n default:y}]
        [-o[utput] {arg name (default:"input")}]
        [-r[eadformat] {char: v or t (default:v)}]
        [-h[elp]

VipLabelContour


------------------------------
VIP Info:
	 Get contour(s) in a label volume from a label or a list of labels
------------------------------
Usage: VipLabelContour
		-i[nput] {image name}
		-l[abel {(int,...) = list of labels to extract (max:256 labels)}
			example : -l 60,250,16,128
		-v[alue {(int,...) = list of corresponding label filling colors (max:256 colors)}
			example : -v 15,245,253,75
			Caution : Number of labels must be equal to number of colors
		[-c[connexity] {(int) = 6, 18 or 26 (default:6)}}
		[-o[utput] {image name (default:"contour")}]
		[-r[eadformat] {char: v or t (default:v)}]
		[-w[riteformat] {char: v or t (default:v)}]
			v=VIDA, t=TIVOLI
		[-h[elp]]
The input and output are label volume file.


VipLabelMatching


------------------------------
VIP Info:
	 Matching from labelled MRI and statistical map image resampling
------------------------------

Usage: VipLabelMatching
		-r[eference] {reference image name}
		-i[nput] {image name}
		[-a[ctivation] {reference statistical map name (default:not used)}]
		[-f[unctionnal] {statistical map name (default:not used)}]
		[-l[abel] {label to match (default:use all label found)}]
		[-o[utput] {image name (default:"resampled")}]
		[-w[riteformat] {char: v, s or t (default:v)}]
			v=VIDA, s=SPM, t=TIVOLI
		[-h[elp]]

VipLabelOverlap


------------------------------
VIP Info:
	 Overlap measurement between structures defined by a label
------------------------------

Usage: VipLabelOverlap
		-r[eference] {reference image name}
		-i[nput] {image name}
		[-l[abel] {reference label (default:use all label found)}]
		[-il[abel] {input image label (default:use same label as reference)}]
		[-h[elp]]

VipLinComb


------------------------------
VIP Info:
	 Computes the linear combination a1*i1+a2*i2
------------------------------

Usage: VipLinComb
        -a1 {float}
        -i1 {image name}
        -a2 {float}
        -i2 {image name}
        [-f[loat]]
The command works with float volumes (reading and writing do the same)
        [-m[ean]]
for a1>0, and a2>0, computes a1*i1+a2*i2/(a1+a2)
        [-o[utput] {image name (default:"lincomb")}]
        [-r[eadformat] {char: v, s or t (default:v)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
        [-w[riteformat] {char: v, s or t (default:v)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
        [-h[elp]

VipLinearResamp


------------------------------
VIP Info:
	 Performs a trilinear resampling of input volume according to template geometry
------------------------------

Usage: VipLinearResamp
        -i[nput] {image name}
        -t[emplate] {header or image name}
        [-f[loat]]
The command works with float input volume (reading and writing do the same)
        -d[eplacement] {deplacement file (rotation or affine}
        [-o[utput] {image name (default:"linresampled")}]
        [-r[eadformat] {char: v, s or t (default:v)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
        [-w[riteformat] {char: v, s or t (default:v)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
        [-l[abel] {char: 0 or m (default:0)}]
Forces the value of samples of the resample image outside to be set to 0(default) or minimmum of the image to resample
        [-h[elp]

VipListLabel

Usage: VipListLabel
        -i[mage]      {image name}

VipMask


------------------------------
VIP Info:
	 Simply mask an image
------------------------------

Usage: VipMask
        -i[nput] {image name}
        -m[ask] {mask name}
        [-f[loat]]
The command works with float input volume (reading and writing do the same)
        [-l[evel]] {int (defines real mask)}
        [-o[utput] {image name (default:"masked")}]
        [-r[eadformat] {char: a, v, s or t (default:any)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
        [-w[riteformat] {char: v, s or t (default:t)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
        [-h[elp]

VipMatching

Surface matching tool
(the program yields several 3D transformations)
      - <refsurf>_TO_<mobsurf>: alignment of the reference image along the mobile one
      - <mobsurf>_TO_<refsurf>: alignment of the mobile image along the reference one

Usage: VipMatching
        -r[efsurf] {image name}
The reference edge image from which is computed the distance map
        -m[obsurf] {image name}
        [-nr[efsurf] {reference image name for deplacement file}]
        [-nm[obilesurf] {mobile image name for deplacement file}]
The mobile surface which is moved through the distance map
        [-gf[ile]] {image name} (default:same as mobile surface)
The mobile surface gradient computed from VipDeriche
        [-gd[im]] <2/3> (default:2)
The gradient dimension (2D or 3D) resulting from VipDeriche
        [-dil[ation]] char: y/n (default:"y")
y : The mobile surface will be inflated to correct for edge localization differences
        [-dis[tmap] {image name (default:"not used")}]
A distance map computed from the reference surface
        [-i[nit]] <deplacement file>
This deplacement (rotation affine) initialized the minimization
        [-dir[ecttransfo]] {file name (default:"<mobsurf>_TO_<refsurf>")}
        [-inv[ersetransfo]] {file name (default:"<refsurf>_TO_<mobsurf>")}
        [-u[ndersampling]] <int> ([1..100] (default:100)
Undersamples (percentage) the mobile surface which speeds up the process
Angle steps:
 First Minimization:
        [-i1[angle]] <float> (Minimization 1, init angle step(default:5.deg)
        [-f1[angle]] <float> (Minimization 1, final angle step(default:0.5deg)
 Second Minimization (including optimal dilation):
        [-i2[angle]] <float> (Minimization 2, init angle step(default:1.deg)
        [-f2[angle]] <float> (Minimization 2, final angle step(default:0.2deg)
 Third Minimization (including optimal dilation and outlier elimination):
        [-i3[angle]] <float> (Minimization 3, init angle step(default:1.deg)
        [-f3[angle]] <float> (Minimization 3, final angle step(default:0.05deg)
        [-t[hreshold]] <float> (outlier) (default:1.7 * mean dist)
 Chamfer mask sizes:
        [-x[masksize]] <int> ((default:5)
        [-y[masksize]] <int> ((default:5)
        [-z[masksize]] <int> ((default:3)
        [-2[D]] <y/n> (default:"n")
Only translations and rotation around Z axis are allowed
        [-R[eadformat] {char: v, s or t (default:v)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
        [-h[elp]

VipMerge


------------------------------
VIP Info:
	 Simply mask an image
------------------------------

Usage: VipMask
        -i[nput] {image name}
        -m[erged] {image name}
        [-f[loat]]
The command works with float input volume (reading and writing do the same)
        [-c[ustomize] {a/l/s (default:a)}]
a: all to value, l: level to value, s: all to same value
        [-l[evel]] {int (level to be merged) (default: not used)}
        [-v[alue]] {int (merged value) (default: input "max+1")}
        [-o[utput] {image name (default:"merge")}]
        [-r[eadformat] {char: v, s or t (default:v)}]
        [-r[eadformat] {char: a, v, s or t (default:any)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
        [-w[riteformat] {char: v, s or t (default:t)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
        [-h[elp]

VipMinimizeInformation


------------------------------
VIP Info:
	 to be writen
------------------------------

VipMoment


------------------------------
VIP Info:
	 Compute moment and moment invariant of a pattern from a label image.
------------------------------
Usage: VipMoment
		-i[nput] {image name}
		-l[abel] {pattern label in image}
		[-o[utput] {ASCII result file (default:output on stdout)}]
			set the file extension to .pca to have a specific
			ASCII file structure for Principal Component Analysis.
			set the file extension to .inv to have a specific
			ASCII file structure for Covariance matrix computation.
		[-t[ype] {n | l (default:n)}]
			n=NORMAL, l=LEGENDRE
		[-d[imension] {2 | 3 (default:3)}]
			2=2D moment, 3=3D moment
		[-r[eadformat] {char: v or t (default:v)}]
			v=VIDA, t=TIVOLI
		[-h[elp]]


VipOpenFold


------------------------------
VIP Info:
	 Apply an homotopic dilation to a hard seed of the brain
------------------------------
The homotopic constraint prevent the merge of two neighboring gyri
In this way, we get better triangulation for 3D rendering
Or better cortex surface representations

Usage: VipOpenFold
        -i[nput] {brain image name}
 a brain segmentation usually obtained with VipGetBrain
 for t algorithm, this image has to include MR gray level values
        [-a[lgo] {string:e/t/i/f (default : e)}]
 e: the hard seed is obtained from a simple binary erosion of the binary brain
 t: the hard seed related to white matter is obtained by a simple thresholding
 i: the hard seed is given by another image
 f: nothing happens apart from filling if trigered
        [-n[iter] {nb iter homotopic dilation (default : 5)}]
 the homotopic dilation follows a 6-connectivity related front based propagation
        [-e[rosion] {algo e : erosion size (default : 2mm)}]
 without c flag, this parameter is in mm, with c falg, it is connectivity related
        [-c[onnectivity] {(erosion) string:6/18/26/4/8/4s/8s/4c/8c (default:not used)}]
        [-t[hreshold] {algo t: int (default : not used)}]
        [-s[eed] {algo i: image name (default : not used)}]
        [-o[utput] {image name (default:"openfold")}]
        [-f[ill] {y/n, fill the fold depth (default: n)}]
This refinement consists in closing the brain, then eroding the closure,
and adding the erosion result to the segmented brain to fill in the depth.
This is done for 3D rendering optimization (less triangles)
        [-fc[losing] {float (mm) closing size for f mode (default: 5)}]
        [-fe[rosion] {float (mm) erosion size for f mode (default: 10)}]
        [-r[eadformat] {char: v or t (default:v)}]
        [-w[riteformat] {char: v or t (default:v)}]
        [-h[elp]

VipOpening


------------------------------
VIP Info:
	 Dilates the object defined as all non zero points
------------------------------
The structuring element is a ball of radius size for a chamfer distance.

Usage: VipOpening
        -i[nput] {image name} : object definition
        -s[ize] {opening size in mm.}
        [-a[lgo] {char: f or t (default:"f")}]
f:bounded thick front propagation, t: chamfer transformation
        [-o[utput] {image name (default:"opened")}]
        [-x[masksize] {int (default:3)}: chamfer mask xsize]
        [-y[masksize] {int (default:3)}: chamfer mask ysize]
        [-z[masksize] {int (default:3)}: chamfer mask zsize]
        [-m[ultfactor] {float (default:VIP_USUAL_DISTMAP_MULTFACT)}]
        [-c[onnectivity] {string:6/18/26/4/8/4s/8s/4c/8c (default:26)}]
Suffixes "s" and "c" means sagittal and coronal orientations
        [-r[eadformat] {char: v, s or t (default:v)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
        [-w[riteformat] {char: v, s or t (default:v)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
        [-h[elp]

VipPca


------------------------------
VIP Info:
	 Principal Components Analysis.
------------------------------
Usage: VipPca
		-i[nput] {data ASCII file}
		[-p[rincipal] {principal axis data file (default:stdout output)}]
			set the file extension to .plot to have a specific
			ASCII file structure for IDL/Matlab plot.
		[-c[ircle] {correlation circle data file (default:stdout output)}]
			set the file extension to .plot to have a specific
			ASCII file structure for IDL/Matlab plot.
		-v[ariables] {number of variables (e.g. number of moments)}
		-t[ests] {number of tests (e.g. number of objects)}
		[-a[nalyse] {c | v | s (default:c)}]
			c=Correlation analysis, v=Variance/covariance analysis
			s=SSCP analysis
		[-h[elp]]


VipPreprocessing


------------------------------
!! VIP Preprocessing Error:
    Execution aborted: Incoherent generic filename: -h (.gen extension required).
------------------------------

VipSetPointValue


------------------------------
VIP Info:
	 Set a particular point to a specified value
------------------------------

Usage: VipSetPointValue
		-i[nput] {image name}
		[-x[coord] {X coordinate of point (default:0)}]
		[-y[coord] {Y coordinate of point (default:0)}]
		[-z[coord] {Z coordinate of point (default:0)}]
		[-v[alue] {int: filling value (default:255)}]
		[-o[utput] {image name (default:"filled")}]
		[-r[eadformat] {char: v, s or t (default:v)}]
		[-w[riteformat] {char: v, s or t (default:v)}]
			v=VIDA, s=SPM, t=TIVOLI
		[-h[elp]]

VipSingleThreshold


------------------------------
VIP Info:
	 Applies a threshold to input image according to << mode >> and << type >>
------------------------------

Usage: VipSingleThreshold
        -i[nput] {image name}
        -t[hreshold] {int (threshold)}
        [-f[threshold]] {float (threshold)}
If flevel is given, level is no more required
        [-o[utput] {image name (default:"thresholded")}]
        [-m[ode] {gt | ge | eq | lt | le | ne (default:ge)}]
gt=GREATER_THAN, ge=GREATER_OR_EQUAL_TO, eq=EQUAL_TO, lt=LOWER_THAN, le=LOWER_OR_EQUAL_TO, ne=NOT_EQUAL_TO
        [-c[olor] {b | g (default:g)}]
Output image nature: b=BINARY_RESULT: ( 255 / 0 ), g=GREYLEVEL_RESULT
        [-r[eadformat] {char: a, v, s or t (default:any)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
        [-w[riteformat] {char: v, s or t (default:t)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
        [-h[elp]

VipSkeleton


------------------------------
VIP Info:
	 Compute a 3D skeleton of the object (usually dedicated to cortical folds)
------------------------------
Default modes are dedicated to the cortex (input comes from VipHomotopicSnake)
In that case, a voronoi related to sulcal root is also proposed.

Usage: VipSkeleton
        -i[nput] {image name} : object definition
        [-so[utput] {image name (default:"skeleton")}]
        [-vo[utput] {image name (default:"rootsvoronoi")}]
        [-sk[eleton] {w/s/0  (default:w)}]
w: the skeletonization is coupled with the watershed idea
   this mode is dedicated to the cortical fold extraction
   this mode requires an image to compute its mean curvature as a ridge detector
   The aim is an homotopic skeleton following the ridges
s: standard homotopic skeletomization
0: no skeletonization
        [-im[mortality] {string:a/s/c/n (default:s)}]
property required to be preserved during the homotopic skeletonization
a: homotopic with full preservation of points, curves and surfaces
s: homotopic with full preservation of points and surfaces
c: homotopic with full preservation of points and curves
n: homotopic with no preservation
        [-fv[oronoi] {y/n  (default:y)}]
Computes a voronoi of the input object corresponding to a sulcal root based parcellisation
this mode requires an image to compute its Gaussian curvature as a saddle point detector
This saddle points represent the anatomical plis de passage
        [-p[rune] {string:c/o/co/0 (default:co)}]
c: homotopic pruning of curves
o: homotopic pruning of outside 6-neighbors
co: c & o
0: no pruning
        [-wp[rune] {int:minimum catchment bassin depth (default:3mm)}]
        [-li[nside] {int:label<290 (default:0)}]
        [-lo[utside] {int:label<290 (default:11)}]
        [-c[lassification] {y/n (default:y)}]
this flag trigered a final topological classification of the skeleton
        [-g[eometry] {image name (default:nothing)}]
--------------------------Mean curvature:-----------------------------------------
with watershed flag trigered, the watershed idea is related to the isophote mean
curvature of this image, which is usually a MR image with segmented brain
but could be the input binary image or a distance map computed from it
In this context, mean curvature is used as a ridge detector
During the first iterations, points whose mc < mcthreshold can not become immortals
This trick helps the skeletonization to get rid of small non significative simple surfaces
The skeletonization itself follows an immersion like process begining above mcthreshold
--------------------------Gaussian curvature:-----------------------------------------
with voronoi flag trigered, this image is used to compute isophote Gaussian curvature
Then points of the gray/white interface whose gc<gcthreshold are marked
The cortical folds are filled in at this location to reduce depth
        [-lz[ero] {(float) lowest mean curvature for watershed (default:0.3)}]
        [-lu[p] {(float) highest mean curvature for watershed(default:1)}]
        [-e[rosion] {(float) wave erosion for watershed (default:0.1)}]
        [-readmc {mean_curvature image name (default:nothing)}]
        [-mcs[igma] {float (mm)  (default:1mm)}]
the sigma of the Gaussian smoothing before mean curvature computation
        [-gcs[igma] {float (mm)  (default:2mm)}]
the sigma of the Gaussian smoothing before Gaussian curvature computation
        [-mct[hreshold] {float (default:0.2)}]
        [-gct[hreshold] {float (default:-0.05)}]
cf. geometry help
        [-ve[rsion] {int, version depending on the hemi_cortex version, 1 or 2 (default: 2)}]
        [-r[eadformat] {char: v or t (default:v)}]
        [-w[riteformat] {char: v or t (default:v)}]
       [-srand {int (default: time}]
Initialization of the random seed, useful to get reproducible results
        [-h[elp]

VipSplineResamp


------------------------------
VIP Info:
	 Performs a spline based resampling of input volume according to template geometry
------------------------------

Usage: VipSplineResamp
        -i[nput] {image name}
        -t[emplate] {image name}
        -th[eader] {template header name (GIS format)}
        [-sx] {float:template vox size x}
        [-sy] {float:template vox size y}
        [-sz] {float:template vox size z}
        [-dx] {int:template dim x}
        [-dy] {int:template dim y}
        [-dz] {int:template dim z}
        [-f[loat]]
The command works with float input volume (reading and writing do the same)
        -d[eplacement] {deplacement file (rotation or affine}
        -d[id] {set deplacement to identity}
Warning, in that case, if the voxel size is different a translation is used
to correct for the fact that our coordinate origin is the first voxel center
        -d[write] {write the deplacement file as input_TO_template}
        [-or[der] {int: [0..7] (default:3)}]
Spline interpolation order:
0 : nearest neighbor
1 : linear
2 : quadratic
3 : cubic
4 : quartic
5 : quintic
6 : galactic
7 : intergalactic
        [-o[utput] {image name (default:"splineresampled")}]
        [-r[eadformat] {char: a, v, s or t (default:any)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
        [-w[riteformat] {char: v, s or t (default:t)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
        [-h[elp]
For more information:
http://bigwww.epfl.ch/thevenaz/interpolation/index.html
M. Unser, Splines: A Perfect Fit for Signal and Image Processing
IEEE Signal Processing Magazine, vol. 16, no. 6, pp. 22-38, November 1999

VipSplit


------------------------------
VIP Info:
	 Split multi-frame volume
------------------------------

Usage: VipSplit
        -i {image name}
        [-f[loat] : the volume is splited with Perfectly scale factor
        [-o[utput] {image name (default:"split")}]
        [-h[elp]

VipSplitBrain

Usage: VipSplitBrain
Try to split the brain into 3 parts: hemispheres and cerebellum.
White matter is segmented first, then cleaned up to prevent cavities
from disturbing morphological processing. Then the standard
Erosion, seed selection, reconstruction skim is used.
The program tries several erosion sizes in order to find the smallest one
which minimizes morphological opening effects. When provided, a template
of the localization of the 3 parts in SPM talairach space is used to select seeds.
Otherwise, simple considerations are used.
You can improve the use of the template if you provide CA, CP, and
a third point of interhemispheric plane
        -i[nput] {MRI (bias corrected) image name}
        [-t[emplate] {voronoi in Talairach: (default: /home2/local/Panabase/demo/talairach/closedvoronoi)}]
a 3 color image with the usual spm bounding box
        [-T[emplateUse] {(y/n), default:y}]
Without template, the result is less reliable but often correct
        [-C[utUse] {(y/n), default:y}]
Delete some points in corpus callosum and stem from Talairach Coord
        [-R[idge] {White ridge image name (default: not used)}]
        [-b[rain] {binary brain image name (default:brain)}]
brain binary mask
        [-o[utput] {splitted brain image name (default:voronoi)}]
a 3 color label image (a voronoi diagram inside brain mask
        [-m[ode] {char: V[oronoi], W[atershed], default:V
Voronoi: classification using voronoi diagramme
Watershed: classification using a watershed algo during the propagation
        [-wa[lgo] {algo r/b/c/t, default:r
r: regulariwed grey white classification
b: barycenter, cf -B option
c: coef, cf -wt and -Coef options
t: direct input of the threshold
        [-wt[hreshold] {algo t: int (default :mW - Coef*sW)}]
The threshold providing white matter after masking by brain mask
mW: white matter mean grey level, sW: standard deviation
        [-ws[eed] {write seed image (y/n), default:n}]
To get an image of seeds and seeds in the template (to understand some problems
        [-Co[ef) {float (default :2)}]
multiplicative factor providing threshold for white matter
        [-B[ary] {float (default :0.75)}]
Factor for barycenter between gray matter (1-Bary) mean and white matter mean (Bary)
        [-e[rosion] {float (default :2mm)}]
Initial erosion size, then step by step increasing by 0.5mm
        [-c[csize] {int (default :500)}]
Connected component minimal size to enter the seed selection process
        [-P[oints] {AC,PC,IH coord filename (*.tal) (default:not used)}]
Correct format for the commissure coordinate file toto.APC:
AC: 91 88 113
PC: 91 115 109
IH: 90 109 53
        [-xA[C] {(int [0-xsize[) AC X coordinate}]
        [-yA[C] {(int [0-ysize[) AC Y coordinate}]
        [-zA[C] {(int [0-zsize[) AC Z coordinate}]
        [-xP[C] {(int [0-xsize[) PC X coordinate}]
        [-yP[C] {(int [0-ysize[) PC Y coordinate}]
        [-zP[C] {(int [0-zsize[) PC Z coordinate}]
        [-a[nalyse] {char y/n/r: automatic histogram analysis, default:y}]
y: do histogram analysis to get mw and sw, r: read input.han,
n: do simpler things
        [-hn[ame] {histo analysis, default:input )}]
read when -a r is set, this file has the .han extension (VipHistoAnalysis)
        [-xI[nterHem] {(int [0-xsize[) Inter-hemis. point X coord.}]
        [-yI[nterHem] {(int [0-ysize[) Inter-hemis. point Y coord.}]
        [-zI[nterHem] {(int [0-zsize[) Inter-hemis. point Z coord.}]
        [-Z[over] {int (default :zCA+10)}]
Without template, subset of the cerebellum part above Zover are deleted
in order to modify the competion between the 3 seeds for influence
        [-r[eadformat] {char: a, s, v or t (default:any)}]
        [-w[riteformat] {char: s, v or t (default:t)}]
        [-srand {int (default: time}]
Initialization of the random seed, useful to get reproducible results
        [-h[elp]
Some more information in:
Shape bottlenecks and Conservative Flow systems
J.- F. Mangin, J. Regis and V. Frouin
IEEE/SIAM MMBIA Workshop (Math. Methods in
Biomed. Image Analysis), San Francisco, IEEE Press
319-328, 1996

VipSubVolume


------------------------------
VIP Info:
	 Extraction of a sub-volume
------------------------------
Usage: VipSubVolume
		-i[nput] {image name}
		-f[loat] y/n {default:no}
Trigers perfect use of vida scale factors
		[-o[utput] {image name (default:"subvolume")}]
		[-x {first X coordinate}] (default:0)
		[-y {first Y coordinate}] (default:0)
		[-z {first Z coordinate}] (default:0)
		[-t {first T coordinate}] (default:0)
		[-X {last X coordinate or sub-volume X-dimension}] (default:SizeX)
		[-Y {last Y coordinate or sub-volume Y-dimension}] (default:SizeY)
		[-Z {last Z coordinate or sub-volume Z-dimension}] (default:SizeZ)
		[-T {last T coordinate or sub-volume T-dimension}] (default:SizeT)
		[-l] {take X,Y,Z and T as dimensions instead of coordinates}
		[-r[eadformat] {char: v or t (default:v)}]
		[-w[riteformat] {char: v or t (default:v)}]
			v=VIDA, t=TIVOLI
		[-h[elp]]


VipSumFrame

Usage: VipSumFrame
		-i[nput] {image name}
		-s[cale] y/n {default:no}
		Trigers perfect use of vida scale factors
		[-o[utput] {image name (default:"summed")}]
		-f[rom] {first frame (default:0)}
		-t[o] {last frame (default:last frame of serie)}
		[-h[elp]]
-----------------------------
VipSumFrame performs for each voxel, the sum 
            of the activity found in volume serie
            starting at 'from' ending at 'to'
            
            .No Decay correction is performed
            
            .Relative dynamic of the different
            frames is accounted for whether -scale
            switch is yes or no.
            .When very different dynamics exist
            between frames '-scale y' is preferable
            for accuracy at a non neglictable 
            computing cost.
            .Only FLOAT and S16BIT data can be processed.
-----------------------------

VipSwapEndian


------------------------------
VIP Info:
	 Swap high and low bytes of a VIDA image
------------------------------
		[-h[elp]]

Usage: VipSwapEndian
		-i[nput] {image name}
		[-o[utput] {image name (default:"swapped")}]
		[-n[bytes] number of bytes involved for swap {integer: 2 or 4 (default:2)}]
			2: AB -> BA;  4, ABCD -> DCBA    (only used with the '-r o' option)
		[-r[eadformat] {char: v, s, t or o (default:v)}]
		[-w[riteformat] {char: v, s, t or o (default:v)}]
			v=VIDA, s=SPM, t=TIVOLI, o=OTHER (single binary file)

VipT1BiasCorrection


------------------------------
VIP Info:
	 Computes a smooth multiplicative field which corrects for non stationarities.

------------------------------
This field aims at minimizing the volume entropy (= minimizing information...).
A tradeoff is found between this entropy and the internal energy of a membrane using annealing.

Usage: VipT1BiasCorrection
        -i[nput] {image name}
        [-o[utput] {image name (default:"nobias")}]
        [-m[ode] {char: s,g (default:g)}]
Switch between various terms to prevent compression of information
s: without g addition
g: minimize variance of white matter ridges
        [-f[ield] {bias field name (default:"biasfield")}]
        [-hW[rite] {write volume for histo estimation: y/n (default:n)}]
        [-hn[ame] {volume for histo estimation image: (default:variance)}]
        [-w[ridges] {white matter ridges image (default:"white_ridges")}]
        [-W[write] {write ridges: y/n/r (default:n)}]
        [-vW[rite] {write variance: y/n (default:n)}]
        [-vn[ame] {variance image: (default:variance)}]
        [-eW[rite] {write edges: y/n (default:n)}]
        [-en[ame] {edge image: (default:edges)}]
        [-mW[rite] {write mean curvature: y/n (default:n)}]
        [-mn[ame] {mean curvature image: (default:mean_curvature)}]
        [-mcs[igma] {float (mm) (default:1mm)}]
the sigma of the Gaussian smoothing before mean curvature computation
        [-Di[mfield] {type of field (2/3) (default:3)}]
2: the correction field is constant by slice, 3: constant by cubes
        [-F[write] {write field: y/n (default:n)}]
        [-d[umb] {y/n (default:y)}]
        [-Ke[ntropy] {float  (default:1.)}]
Weight of the volume entropy which will be multiplied by the field size
        [-Kr[egul] {float  (default:50.)}]
Weight of the membrane/spline energy (sum of the squared log of the ratio between 6-neighbors)
        [-Ko[ffset] {float  (default:0.5)}]
Weight of the squared difference between old and new mean
        [-Kc[rest] {float  (default:20.)}]
Weight of the voxel in the white ridge volume
        [-c[ompression] {int [0,14]  (default:auto)}]
The number of bits which are discarted during the volume entropy computation (= /2^compression))
        [-t[auto] {char: y/n default:n}]
        [-tl[ow] {int (default:3*2^compression)}]
        [-th[igh] {int (default:not used)}]
        [-e[dges] {int (default:not used, else n/2/3)}]
remove 2D/3D edges for histogram estimation (discard partial volume)
        [-vt[ariance] {int (default:not used, else int threshold)}]
high threshold on standard deviation in 26-neighborhood for inclusion in histogram
Values beyond this threshold are not taken into account.
In return, the field correction is applied to all values to get the final result
        [-vp[ourcentage] {int (default:75, else int threshold)}]
Pourcentage of non null points kept with a ranking stemming from local variance
        [-T[emperature] {float (default:10.)}]
Initial temperature for annealing
        [-G[rid] {int (default:2)}]
Number of grid for minimization (annealing on the highest only)
        [-g[eometric] {float (default:0.97)}]
Geometric decreasing for annealing schedule
        [-s[ampling] {float  (default:16mm)}]
The sampling of the field: one value for a parallelepipedic volume of points.
In each direction, the sampling is: sampling/DirVoxelSize.
The field is a 0-order spline during optimization (piecewise constant)
               3-order spline during the final bias correction (piecewise linear)
        [-n[Increment] {int (default:2)}]
Minimization is performed using a Gibbs sampler or a ICM (deterministic) approach with
several multiplicative increments are tires for each field point:
1/I^n,...,1/I,I,...I^n:
        [-I[ncrement] {float (default:1.03)}]
elementary multiplicative increment (see above):
        [-a[mplitude] {float ]1,10]  (default:1.1)}]
The field random initialization is in the range [1/amplitude, amplitude]
        [-Z[regulTuning] {float  (default:1)}]
Multiplicative factor for regularization in z direction (bad coil)
        [-L[ast] {int (default:0)}]
Mask the Last last slices in all estimation (for field of view going to the shoulder)
        [-P[oints] {AC,PC,IH coord filename (*.tal) (default:not used)}]
Correct format for the commissure coordinate file toto.APC:
AC: 91 88 113
PC: 91 115 109
IH: 90 109 53
        [-Dk[eep] {float (default:75.0)}]
Mask slices more than Dkeep mm below commissure points
        [-Dc[orrect] {Do the biais correction: y/n (default:y)}]
Write the images as hfiltered or whiteridge whithout doing the bias correction if it has been done by another software
        [-pv[ariance] {float (default:0.05)}]
Preliminary brain mask computation: this percentage of maximal variance might be used as threshold.
Value may need being changed depending on image contrast.
        [-Ct[hreshold] {float (default:-0.4)}]
Threshold on mean curvature. Used to compute white ridges.
        [-Cm[ethod] {string: HE, LE (default:LE)}]
Method for thresholding mean curvature (higher or equal, lower or equal)
        [-S[pecie] {string: H[uman], M[acaca] (default:H)}]
        [-Cw[eight] {string: T1, T2 (default:T1)}]
        [-r[eadformat] {char: a, v, s or t (default:any)}]
        [-w[riteformat] {char: v, s or t (default:t)}]
        [-srand {int (default: time}]
Initialization of the random seed, useful to get reproducible results
        [-h[elp]
More information in:
Entropy minimization for automatic correction
of intensity non uniformity, J.-F. Mangin,
MMBIA (Math. Methods in Biomed. Image Analysis),
Hilton Head Island, South Carolina, IEEE Press
162-169, 2000

VipTalairachCoordinates


------------------------------
VIP Info:
	 Provide the coordinates of a point in the Talairach frame.
------------------------------
Usage: VipTalairachCoordinates
		-X {input point X}
		-Y {input point Y}
		-Z {input point Z}
		-xa[c] {AC point X}
		-ya[c] {AC point Y}
		-za[c] {AC point Z}
		-xp[c] {PC point X}
		-yp[c] {PC point Y}
		-zp[c] {PC point Z}
		-xh[emi] {Hemispheric point X}
		-yh[emi] {Hemispheric point Y}
		-zh[emi] {Hemispheric point Z}
		[-h[elp]]


VipTalairachTransform


------------------------------
VIP Info:
	 Computes the Talairach referential and writes a transformation matrix file from a .APC commissures file
------------------------------
Usage: VipTalairachTransform
        -i[nput] {commissures file name (.APC)}
        -o[utput] {transformation file name (.trm)}
        -m[ask] {brain mask file name, must includes hemispheres only (no cerebellum) - if a voronoi (with cereb) is provided, use the -v option too}
        [-v[oronoi]]
        [-h[elp]
        in voronoi mode, the mask in thresholded to exclude label 3 (cerebellum) from a standard Vip voronoi image


VipTopoClassifMeaning


------------------------------
VIP Info:
	 Gives the meaning of a topological classification value
------------------------------

Usage: VipTopoClassifMeaning
        -v[alue] {int value}
        -a[ll]
        [-h[elp]

------------------------------
!! VIP Error:
	 value arg is required by VipTopoClassifMeaning
------------------------------
Usage: VipTopoClassifMeaning
        -v[alue] {int value}
        -a[ll]
        [-h[elp]

VipTopoClassification


------------------------------
VIP Info:
	 Topological classification of a given label
------------------------------

Usage: VipTopoClassification
		-i[nput] {image name}
		[-o[utput] {image name (default:"classified")}]
		[-l[abel] {label to classify (default:255)}]
		[-r[eadformat] {char: v, s or t (default:v)}]
		[-w[riteformat] {char: v, s or t (default:v)}]
			v=VIDA, s=SPM, t=TIVOLI
		[-h[elp]]

VipTransform


------------------------------
VIP Info:
	 Translation, scale, and rotation volume transformation.
------------------------------
Usage: VipTransform
		-i[nput] {volume name}
		[-o[utput] {transformed volume file (default:"transfo")}]
		[-xs[cale] {X scale factor (default=1.0)}]
		[-ys[cale] {Y scale factor (default=1.0)}]
		[-zs[cale] {Z scale factor (default=1.0)}]
		[-xt[ranslate] {X translation value (default=0.0)}]
		[-yt[ranslate] {Y translation value (default=0.0)}]
		[-zt[ranslate] {Z translation value (default=0.0)}]
		[-xr[otate] {X rotation angle in degree (default=0.0)}]
		[-yr[otate] {Y rotation angle in degree (default=0.0)}]
		[-zr[otate] {Z rotation angle in degree (default=0.0)}]
		[-xg[ravity] {X rotation center position (default=dimx/2)}]
		[-yg[ravity] {Y rotation center position (default=dimy/2)}]
		[-zg[raviy] {Z rotation center position (default=dimz/2)}]
		[-h[elp]]


VipTriangle


------------------------------
VIP Info:
	 to be writen
------------------------------

VipVFilter


------------------------------
VIP Info:
	 Apply a V-Filter to an image
------------------------------

Usage: VipVFilter
		-i[nput] {image name}
		[-o[utput] {image name (default:"vfilter")}]
		[-m[masksize] {int (default:2)}]
		[-t[ype] {char: o or n (default:o)}]
			o=OPTIMIZED, n=NON OPTIMIZED
		[-r[eadformat] {char: v, s or t (default:v)}]
		[-w[riteformat] {char: v, s or t (default:v)}]
			v=VIDA, s=SPM, t=TIVOLI
		[-h[elp]]

VipVoiStat

		----------------------------------------------
		VipVoiStat performs statistics computation
			given a VOI file (label) a serie file
			a displacement file (and 
			possibly a movment compensations)
		
		Flag --pvec_matrix triggers pvec correction
			in that case the voi file must contain the 
			background region (default label is 200 or
			given by --pvec_bkg_label
			the -v[oi] parmater is the -l[abelout] file
			output by the VipStriataGTM command
		----------------------------------------------
		
Usage : VipVoiStat
		-s[serie] {dynamic serie}
		-v[oi]    {voi volume}
		-d[epla]  {deplacement file (rotation/ affine}
		[-c[urve] {ASCII result file (def: stdout)}]
		[--dmc  {file with movement compensation}]
		[--pvec_matrix (pv cor y/n, default:y)]
		[--pvec_bkg_label (label of bkg, default:200)]
		[-h[elp]]

VipVoronoi


------------------------------
VIP Info:
	 Computes a (generalized) Voronoi diagram for the different seeds in input
------------------------------
Underlying distance either corresponds to a Euclidean-like chamfer distance .
or corresponds to the distance related to the specified connectivity.

Usage: VipVoronoi
        -i[nput] {image name} : object definition
        [-o[utput] {image name (default:"distmap")}]
        [-di[stmap] {image name (default:"distmap")}]
        [-wd[istmap] {'y' or 'n' (default:'n')}]
write the underlying distance map
        [-c[onnectivity] {string:6/18/26/4/8/4s/8s/4c/8c (default:not used)}]
        [-g[eodesic] {string:'i' or 'f' (default:not used)}]
geodesic distance map: 'i':iterated chamfer transform
                       'f':thick front propagation
        [-d[omain] {int (default:0)}]
this value defines propagation domain for the geodesic distance
        [-f[orbiden] {int (default:-1)}]
this value defines outside of domain for the geodesic distance
        [-n[itermax] {int (default:5)}]
maximum number of iterations for iterated chamfer transform
Suffixes "s" and "c" means sagittal and coronal orientations
        [-x[masksize] {int (default:3)}: chamfer mask xsize]
        [-y[masksize] {int (default:3)}: chamfer mask ysize]
        [-z[masksize] {int (default:3)}: chamfer mask zsize]
        [-m[ultfactor] {float (default:50)}]

------------------------------
VIP Info:
	 Read and Write flag are actually configured for debugging...
------------------------------
        [-r[eadformat] {char: v or t (default:v)}]
        [-w[riteformat] {char: v or t (default:v)}]
        [-h[elp]

vip_test_well_composed_configurations


vip_test_well_composed_topology


AimsTopHat


    AimsTopHat
    ----------

Morphological operators
for both binary and gray level intensity images

Options :

[ -i <file name (read only): { Volume of DOUBLE, Volume of FLOAT, Volume of S16,
    Volume of S32, Volume of S8, Volume of U16, Volume of U32, Volume of U8 }>
    Input image ]

[ -r <FLOAT> ]
    Radius in mm

[ -m <string> ]
    Mode that can be:
    
    ero --> erosion
    dil --> dilation
    clo --> closing
    ope --> opening
    thc --> top-hat by closing
    tho --> top-hat by opening

[ -e <string> ]
    Morphology of the structuring element:
    
    iso --> isotropic
    ani --> anisotropi - much slower
    cub --> cubic 
    3pl --> along 3 orthogonal planes
    pla --> along ortho & slant planes - slower
    sag --> 3 planes around sagittal axis (half radius along and tangential to
    axis)

[ -recons <boolean> ]
    Reconstruction (cubic opening,closing,top-hat only) :
    1 --> reconstruction is active (default inactive)

[ -mask <FLOAT> ]
    mask value (no morphological computation for this value)  :
    -998 --> no mask (default)

[ -b <FLOAT> ]
    Border value : -999 = automatic (default)

[ -y0 <S32> ]
    sagittal axis y location for 'sag' mode only (default : dim(Y)/2)

[ -z0 <S32> ]
    sagittal axis z location for 'sag' mode only (default : dim(Z)/2)

[ -o <string> ]
    Output image

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


BabyBrainHemiCut

usage : Masking of the interhemispheric fissure
	-i[nput] {string} {input volume name without suffix}
	-a[cpc] {string} {ACPC plane file}
	-ro[utput] {string} {output file name without suffix for right hemisphere) }
	-lo[utput] {string} {output file name without suffix for left hemisphere ) }
	[-dist[fromplane] {float} {masking distance from ACPC plane; overlap if negative (default:+5 mm)}]
	[-d[ebug] {bool} {debug mode (0:OFF 1:ON, default=0)}]

BabyBrainIntensityRange

Usage: extraire_plage_WM_GM_v2 
	-i {string} {input volume name without suffix}]
	-o {string} {output mask volume without suffix}]
	-h {string} {output histo name (default:input_name.histo)}]
	-q {int} {quantif size for histogram (default:50)}]

BabyCGNCerebSeg

Usage: Segmenting_CGN_from_Cerebellum 
	-i[nput] {string} {Central Grey Nuclei and Cerebellum GIS file (without extension)}
	-dyn[amic] {float} {minimum percent dynamic (default: 10 pct)}
	-a[cpc] {string} {ACPC plane file}
	-o[utput] {string} {Output segmentation file (1=Central Grey Nuclei, 2=Cerebellum}
	[-d[ebug] {bool} {debug mode (0:OFF 1:ON, default=0)}]

BabyCGNDetection

Usage: cgn_detection 
	-i[nput] {string} {input mri name without suffix}
	-m[ask] {string} {input mask name without suffix}
	-o[utput] {string} {output volume name without suffix}
	[-r[adius_ratio] {float} {radius ratio of the ellipsoid (in mm) (default: 1.2 mm)}]
	[-s[tdev_ratio] {float} {standard deviation ratio for the CGN highest intensity (default:1)}]
	[-d[ebug] {boolean} {1:debug mode 0:no debug (default)}]
	 It detects hemispheric central grey nuclei (CGN) based on its bounding ellipsoid and its intensity values

BabyDetectorNormalization

Usage: normaliserDetecteur 
	-i[nput] {string} {input volume name without suffix}
	-o[utput] {string} {output volume name without suffix}
	[-min] {float} {min threshold value (default:0)}
	[-max] {float} {max threshold value (default:0)}
	[-type] {int} {normalisation type 0:linear; 1:sigmoid  (default:linear)}
	[-scale] {int} {scale for output image (default:1)}
	[-ratio] {int} {sigmoid ratio for sigmoid normalisation only (default:10)}
	Normalizing detector output.

BabyHistoAnalysis

usage : analyse_histo_pourcent <histo in> <fic analyse> <pourcent a droite> [<seuil masque> <domaine masque>] 
	<seuil masque> valeur seuil du masque
	<domaine du masque> ='i','d','s' (default='d') prise en compte des valeurs strictement inferieures,
	   		 differentes ou superieures au seuil

BabyInterFissureMask

usage : interFissureMask (masking of the interhemispheric fissure	-i[nput] {string} {input volume name without suffix(2 oct)}
	-p[oint] {string} {ACPC plane file }
	-o[utput] {string} {output file name without suffix }
	[-d[istfromplane] {int} {masking distance from ACPC plane (default:3 voxels)}]

VipInfantHomotopicSnake


------------------------------
VIP Info:
	 Homotopic segmentation of infant cortex gray/white interface

------------------------------
The result is endowed with a sphere homotopy 

Object has 26-connectivity and background has 6-connectivity 

Specific parameters for single Snake :
	forbidden zone : it has to be within background for snake dilation 
		and in  
 
 
 
 
 
 
 
 
 

Usage: VipInfantHomotopicSnake
        -i[nput] {detection image name}
        -ma[sk] {object mask/potential image name}]
        -ex[ternal_mask] {external mask name for coupled snakes only}]
        [-o[utput] {image name (default:"WMInternalInterface")}]
        [-o2 {image name for coupled propagation (default:"WMExternalInterface")}]
        [-d[eformation] {enum: deformation mode (default=1:object dilation 2:object erosion 3:coupled propagation(object is outside)}]
        [-object {int:label (default:255)}]
        -mo[bject] {float}
        -so[bject] {float}
        [-ko[bject] {float potential (default:24)}]
        -[background {int:snake domain label (default:0)}]
        -mb[ackground] {float}]
        -sb[ackground] {float}]
        [-kb[ackground] {float potential (default:10)}]
        [-ls[peed] {int: low speed constant (default:4)}]
        [-hs[speed] {int: high speed constant (default:12)}]
        [-ir[egularization] {int: inner regularization constant (default:20)}]
        [-or[egularization] {int: outer regularization constant (default:16)}]
        [-f[orbidden] {int:forbidden field label (default:128)}]
        [-oinit {bool:1=init an object at volume border for single snake ONLY (default:0:no init)}]
        [-conn[ectivity] {int:6=conn6 26=conn26 (default:26)}]
        [-niter    {int: number of iterations for snake (default:100)}]
        [-r[eadformat] {char: v or t (default:v)}]
        [-w[riteformat] {char: v or t (default:t)}]
        [-h[elp]

neurlearn

bin/neurlearn: invalid option -- 'h'
usage: bin/neurlearn [-b] [-r] [-e eta] mlp_network.net patterns.pat ncycles
(re-writes the input network)
-b: boolean mode: also print errors in binary classifier mode
-r: reset network before learning (otherwise continues previous learning
-e eta: learn factor [default: 0.1]

neurmakenet

usage: bin/neurmakenet output.net n0 n1 [n2...]
generates a MLP .net file
n0, n1, ...: numbers of cells on each layer - 2 layers minimum are required (inputs and outputs)

neurpatimport

usage: bin/neurpatimport [-r] input [output] [norm_patters]
default output: input.pat
imports an ASCII text file and converts it to a SNNS pattern file (.pat)
-r            :  rescale data
norm_patterns :  use normalization figures from given file

readFolds

-h : No such file or directory

siChangeModels


    siChangeModels
    --------------

Replaces models in some model elements according to a matching criterion on a
specific attribute

Options :

[ -p <string> ]
    input parameters file (tree format) (richer than other parameter given on
    the commandline)
    Parameter file attributes:
    
    mgraph		string	!
    attribute	string
    pattern		string	!
    model		string	!

[ -g <string> ]
    model graph file

[ -a <string> ]
    model attribute to discriminate on

[ -e <string> ]
    regular expression to match model elements for changes

[ -m <string> ]
    model file to replace matched models (.mod)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


siCopyModelDescriptors.py

Usage: Get all descriptors from a model and set it into an  other model.

Options:
  -h, --help            show this help message and exit
  -f FILTER, --labelsfilter=FILTER
                        only models matching this filter are covered.ex :
                        'label1,label2' or 'label' or 'regexp1,regexp2' (here
                        order is important)
  --filtermode=FILTER   strict, flexible or regexp
  -s MODEL, --src=MODEL
                        model file name (default : model.arg)
  -d MODEL, --dst=MODEL
                        model file name (default : model.arg)

siCopyNames

usage : 
bin/siCopyNames namedGraphFile unnamedGraphFile [newFile=unnamedGraphFile]

copies names / labels from an old or incomplete graph file
to a new one without names / labels


siCsvMapGraph.py

Usage: Map csv values onto sulci.

Options:
  -h, --help            show this help message and exit
  -g FILE, --graph=FILE
                        data graph
  --label-attribute=STR
                        'name' or 'label' (default: name)
  -m FILE, --mesh=FILE  grey/white mesh in the same space of the input graph
  --csv=FILE            csv file
  --summary-csv=FILE    summary csv file (one line per sulci)
  -f, --format          print csv format
  -t FILE, --translation=FILE
                        translation file (.trl), or nomenclature file (.hie),
                        or selection file (.sel) (default :
                        /volatile/riviere/brainvisa/build-stable-qt5/share
                        /brainvisa-share-4.6/nomenclature/translation/sulci_mo
                        del_2008.trl)
  --log                 add log (neperian) of mean values read in the input
                        csv
  --log10               add log10 of mean values read in the input csv
  -c COLUMNS, --column=COLUMNS
                        column number to be used in the csv file
  -o OPERATOR, --operator=OPERATOR
                        operator to apply to summarize multiple values on the
                        same sulcus. The default is "mean", but could be "min"
                        or "max"

siDiffModels.py

Usage: Compare two sigraph models.

Options:
  -h, --help            show this help message and exit
  -f FILTER, --labelsfilter=FILTER
                        only models matching this filter are covered.ex :
                        'label1,label2' or 'label' or 'regexp1,regexp2' (here
                        order is important)
  --filtermode=FILTER   strict, flexible or regexp
  -1 MODEL, --model1=MODEL
                        model file name (default : model.arg)
  -2 MODEL, --model2=MODEL
                        model file name (default : none)
  -g FILE, --graph=FILE
                        data graph file name
  --hist=HIST           make histogram from classifiation/regression ratesof
                        models. HIST should be a format supported by pylab
  -p PCT, --pct=PCT     percentage of the biggest differences between models
                        ex : 5.6%, 5.6, 5 (default : 10)
  -c CMP, --cmp=CMP     compared data : a list of compared elements taken in
                        raw, mean, good, bad (default : raw,mean,good,bad)
  -m MODE, --mode=MODE  return biggest or smallest values (default : biggest)
  -a, --abs             compare absolute differences (default : disabled)
  --anatomist           Display first compared value on a graph under
                        anatomist software (default : disabled)

siDisplayGraph.py

Usage: Display graphs with usefull representations.
Usage : siDisplayGraph.py [Options] graph1.arg graph2.arg ...

Options:
  -h, --help            show this help message and exit
  -t FILE, --translation=FILE
                        translation file (default :
                        /volatile/riviere/brainvisa/build-stable-qt5/share
                        /brainvisa-share-4.6/nomenclature/translation/sulci_mo
                        del_noroots.trl)
  -m FILE, --mode=FILE  wireframe, gravity_centers, sulci_gravity_centers,
                        hull_line, bivariate_spline,extremity1, extremity2,
                        hull_intersection, pure_cortical,
                        diff_gravity_centers, centerdist_cortical,
                        markov_relations
  -d DIR, --dir=DIR     directory with siMorpho output files (used by
                        extremities mode).
  -s LIST, --sulci=LIST
                        display only specified sulci.
  -w, --write           Write meshes
  --rewrite-graphs      if specified, input graphs may be modified

siDisplayGrid.py

Usage: Generate diagrams based on grid optimization.

Options:
  -h, --help            show this help message and exit
  -f FILTER, --labelsfilter=FILTER
                        only models matching this filter are covered.ex :
                        'label1,label2' or 'label' or 'regexp1,regexp2' (here
                        order is important)
  --filtermode=FILTER   strict, flexible or regexp
  -m MODEL, --model=MODEL
                        model file name (default : model.arg)
  --max                 best value is the maximum one (default : min)
  --svg                 generate svg diagrams (default : eps)
  -a, --all             generate all optimization grids
  -v VERBOSE, --verbose=VERBOSE
                        level of verbosity

siDivNameList

usage :
bin/siDivNameList [-p prefix] n directory savefile
bin/siDivNameList [-p prefix] -c directory savefile n1 n2...

Divise une liste de modèles (fichiers .mod dans le directory
 donné) en n expressions régulières. Les expressions crées sont
 sauvées dans les fichiers savefile.0, savefile.1 ...
savefile.(n-1)

    -p   enlève le préfixe donné aux noms de fichiers avant 
         de construire les expressions régulières
    -c   mode cpu, donne une liste d'indices correspondant chacun
         à la puissance CPU de la machine concernée

siDomTrain

usage : 
bin/siDomTrain paramFile
bin/siDomTrain [-uncb] modelFile.arg graphFile1.arg ... graphFileN.arg

Learning of validity domains of a model graph.

-u : (uninitialized) don't initialize domains before learning
-n : (nosave) don't save results
-c : (clean) eliminates afterwards unused model elements
-b : (no buckets) don't load buckets (by default, they are loaded)

siEnergy


    siEnergy
    --------

Energy of a labelled graph
In verbose mode, potentials of each individual clique is displayed

Options :

-m <string>
    model graph

-i <string>
    data graph

[ -w <FLOAT> ]
    weight factor (0: keep as is (default), <0: remove existing weights
    according to neighbours number)

[ -t <string> ]
    labels translation file

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


siError


    siError
    -------

Count labelling differences on auto/manual recognitions on a cortical folds
graph. Graph must be labelled manually ("name" attribute) and automatically
("label" attribute)

Options :

[ -i <string> ]
    data fold graph

-l <string>
    labels translation file

[ -r <string> ]
    reference graph name to compare labels with (default: same as input data
    graph)

[ -a <string> ]
    automtic labeling attribute (default: "label")

[ -m <string> ]
    manual (reference) labeling attribute (default: "name")

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


siErrorLightWrapper.py

Usage: Call siError on graph inputs and store resulting error rate in a new entry of a CSV file.

Options:
  -h, --help            show this help message and exit
  -m FILE, --model=FILE
                        graph model
  -l FILE, --labeled_graph=FILE
                        labeled graph file (evaluated one)
  -t FILE, --labels_translation=FILE
                        labels translation file
  -b FILE, --base_graph=FILE
                        base graph file (reference) If not specified,
                        labeled_graph is taken
  -c CSV, --csv=CSV     file storing error rate
  -n NAME, --graph_name=NAME
                        graph name to be stored in CSV
  -a, --append          append errors at the end of an existing files instead
                        of erasing it

siErrorStats


    siErrorStats
    ------------

Counts differences between 'label' and 'name' attributes (automatic and manual
sulci identifications), sulcus by sulcus, and saves a tree with stats in
'resultfile.tre'

Options :

[ -c <string> ]
    parameters file (if you don't provide other parameters on the commandline
    options). You have to provide either this parameters file, or the other
    arguments (result tree file, input graphs)

[ -o <string> ]
    result tree which will contain the difference stats

[ -i <vector of string> ]
    Graphs to count differences from

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


siFlip


    siFlip
    ------

Flips coordinates attributes to appear as the other hemisphere in cortical
folds graphs

Options :

-i <string>
    input graph file

[ -o <string> ]
    output (flipped) graph file

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


siFoldGraph2vrml.py

Usage: Convert Aims data fold graph to vrml1 format.
       siFoldGraph2vrml.py -i input.arg -o output.vrml [OPTIONS]

Options:
  -h, --help            show this help message and exit
  -t FILE, --translation=FILE
                        translation file (default :
                        /volatile/riviere/brainvisa/build-stable-qt5/share
                        /brainvisa-share-4.6/nomenclature/translation/sulci_mo
                        del_noroots.trl)
  -i FILE, --input=FILE
                        data fold graph
  -o FILE, --output=FILE
                        vrml file
  --label-mode=STR      'name': manual label, 'label': automatic label
                        (default: name)
  --hierarchy=FILE      hierarchy (links between names and colors), default :
                        /volatile/riviere/brainvisa/build-stable-qt5/share
                        /brainvisa-share-4.6/nomenclature/hierarchy/sulcal_roo
                        t_colors.hie

siFunctionalGraphs


    siFunctionalGraphs
    ------------------

Analyse les resultats d'un protocole fonctionnel a partir du fichier de config
utilise pour etiqueter les graphes

Options :

-i | --input <string>
    config.tree

-o | --output <string>
    test.hie

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


siGenerateLearningTasks.py

Usage: Generate a file of learning tasks. Each line represents a call to siLearn command on a particular model.

Options:
  -h, --help            show this help message and exit
  -f FILTER, --labelsfilter=FILTER
                        only models matching this filter are covered.ex :
                        'label1,label2' or 'label' or 'regexp1,regexp2' (here
                        order is important)
  --filtermode=FILTER   strict, flexible or regexp
  -m MODEL, --model=MODEL
                        model file name (default : model.arg)
  -e MAIL, --email=MAIL
                        (default : )
  -p MODE, --parallelism-mode=MODE
                        ['cath', 'duch', 'LSF', 'grid', 'somaworkflow']
                        (default : duch)
  -o FILE, --output=FILE
                        output file name storing tasks (default :
                        learningtasks) or pattern when several files are
                        generated (LSF, cath) : output files are named
                        $pattern1, $pattern2...
  -c FILE, --config=FILE
                        silearn config file (default : siLearn-read.cfg)
  -t TIME, --time=TIME  format : hh:mm (default : 00:30 (30 min))
  -b FILE, --bin=FILE   siLearn binary (default : siLearn.py)

siGraph2Label


    siGraph2Label
    -------------

Create a volume of label from a graph and a file translation.txt  (bucket:
aims_bottom, aims_ss, or aims_junction + syntax hull_junction) 

Options :

-g | -graph | --graph <string>
    input graph

[ -tr | -translation | --translation <string> ]
    tranlslation file, labels are translated according to this dictionary if it
    is provided

[ -tv | -template | --template <string> ]
    template volume: used to set label volume dimensions and voxel size. Note
    that a resampling takes place if voxel sizes differ between graph and
    output volume.

-o | -output | --output <string>
    output volume

[ -b | -bucket | --bucket <vector of string> ]
    bucket name[s]

[ -s | -syntax | --syntax <vector of string> ]
    syntax[es] of bucket

[ -a | --attribute <vector of string> ]
    attributes list that contain a label [default: 'label', 'name' ]

[ -l | --label <vector of string> ]
    label values to be kept (filter) [default: all]

[ -it | --intrans <string> ]
    input int/label translation file. If provided, it will be used for the
    label mapping, and completed if needed

[ -ot | --outtrans <string> ]
    output int/label translation file [default: not saved]

[ --talairach <boolean> ]
    apply internal Talairach transform (prior to other coordinates transform if
    specified). Note that Talairach transform is centered on 0 and will end up
    with most of the brain outside of the output volume if used alone without
    an additional translation.

[ --transform <file name (read only): AffineTransformation3d> ]
    apply the given coordinates transformation (.trm file), after Talairach
    transform if --talairach is also used

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


siGraphSwithNameLabel.py

Usage: Switch label and names values

Options:
  -h, --help            show this help message and exit
  -i FILE, --ingraph=FILE
                        input data graph
  -o FILE, --outgraph=FILE
                        output data graph (default : input)

siGraphToCsv.py

Usage: measure nodewise features and compute their means over sulci labels of several graphs
./siGraphToCsv.py [OPTIONS] graph1.arg graph2.arg...

Options:
  -h, --help            show this help message and exit
  -t FILE, --translation=FILE
                        translation file (default :
                        /volatile/riviere/brainvisa/build-stable-qt5/share
                        /brainvisa-share-4.6/nomenclature/translation/sulci_mo
                        del_noroots.trl)
  -f LIST, --features=LIST
                        features list (comma separated) at node level. Only
                        floating data is supported.
  --all-csv=FILE        csv file storing all measures
  -c FILE, --csv=FILE   csv file storing measured means

siLearn

usage : 
bin/siLearn paramFile
bin/siLearn [-l labelsMapFile] [-n] [-u] [-s] [-c cycles] modelFile trainschemeFile graphFile1.arg ... graphFileN.arg

Learns a model graph

paramFile        :  parameters file for inputs for the command 
                    (Tree file)
-l labelsMapFile :  correspondance map from labels of the 
                    graph to learn to those used by the model
                    (default: sillons_modele.def)

-n               :  (nosave) do not save the model after learning
-u               :  (uninitialized) do not reinitialize the model
                    before learning
-s               :  (stats) initializes learning of stats
-a attr          :  label attribute used to get labels from:
                    usually 'label' or 'name', 'auto' means try 
                    first label, and if no label is present, take 
                    name [default:auto]'
-c cycles        :  number of learning and testing cycles over the
                    graph set while database generation
                    (default: 1)

modelFile.arg  :  model graph file to train
trainschemeFile  :  learning sequence description file
graphFile1.arg .. graphFileN.arg    :  graphs to learn


Signal handlers:
SIGINT (kill -2) (Ctrl-C) : prompt for save, then exits
SIGSEGV, SIGBUS, SIGILL (kill -9,10,11) (error) : save and exit
SIGUSR1 (kill -16) : save and continues learning

WARNING -- Commandline-options are not being maintained any
longer. Use config file for new params.


siLearn.py

Usage: siLearn.py [Options] [silearn.cfg]

Options:
  -h, --help            show this help message and exit
  -f FILTER, --labelsfilter=FILTER
                        only models matching this filter are covered.ex :
                        'label1,label2' or 'label' or 'regexp1,regexp2' (here
                        order is important)
  --filtermode=FILTER   strict, flexible or regexp
  --label_attribute=ATTR
                        label attribute used to get labels from: usually
                        "label" or "name", "auto" means try first label, and
                        if no                 label is present, take name
                        [default:auto]
  --debug               enable debug [default: disable]

siLyxErrors

usage : 
bin/siLyxErrors resultfile.lyx resultfile.tre [dir]
dir: directory où seront écrites les images .eps

Ecrit les tableaux d'erreurs dans un fichier au format LyX
Ces erreurs doivent avoir été calculées avec siErrorStats


siMakeColoredHierarchy


    siMakeColoredHierarchy
    ----------------------

Build colored hierarchy from p-value table.

Options :

-p | --palette <string>
    Input RGV palette image.

-i | --input <string>
    Input statistic file.

-o | --output <string>
    Output hierarchy

[ -s | --suffix <string> ]
    Suffix (eg. _left or _right) (default = none)

[ -t | --transparancy <S32> ]
    Transparancy for values less than min (default = none)

[ -T | --Transparancy <S32> ]
    Transparancy for values greater than max (default = none)

[ -b | --biggest <boolean> ]
    Choose the biggest value (instead of the smallest value) in case of
    multiple possibility (default: false)

[ -k | --keepline <boolean> ]
    Keep the first line (i.e. header) of the file (default: false)

[ -inv | --invert <boolean> ]
    Invert label/name  (default: false)

[ -g | --graph <string> ]
    Hierarchy graph syntax (default = CorticalFoldArg)

[ -M | --Max <FLOAT> ]
    Maximum palette value (default = auto).

[ -m | --min <FLOAT> ]
    Minimum palette value (default = auto).

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


siMakeModel


    siMakeModel
    -----------

Creates a sulcal model graph

Options :

-o <string>
    output model filename (.arg)

-l <string>
    labels translation filename

-m <string>
    template node model filename (.mod)

-d <string>
    template domain filename (.dom)

[ -f <string> ]
    fallback node model filename (.mod) used for unknown situations ('-' can be
    specified for none for compatibility with older sigraph releases)

[ -r <string> ]
    fallback relation model filename (.mod)

[ --mversion <string> ]
    model version [default: 4.6]

[ --dversion <string> ]
    data graphs compatibility version [default: 3.1]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


siMakeParcellationHierarchy


-------------------------------------------------------------------------
siMakeParcellationHierarchy   -g[yrus] <output gyrus hierarchy>          
                              -s[ulcus]<output sulcus hierarchy >        
                              -m[odel] <intput gyri model >              
                              -l[evel] <level model>		            
                              [-h[elp]]                                  
-------------------------------------------------------------------------
 Make sulci and gyri hierarchy for parcellation                          
-------------------------------------------------------------------------
	gyri model          : Choice of the sulcus/sulcus relations ('*.gyr')
     level model         : Choice of the level of description file ('*.trl')  
-------------------------------------------------------------------------

siMergeModels


    siMergeModels
    -------------

Merges two model graphss by taking the best elements of each

Options :

-i <string>
    1st model graph

-j <string>
    2nd model graph

-o <string>
    output model graph

[ -f <DOUBLE> ]
    comparison factor: a model from the 2nd graph will replace the one in the
    1st one if conf1 < conf2 * factor, conf1 and conf2 being the confidence
    factors of both models [default: 1]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


siMeshSulciOperture


-------------------------------------------------------------------------
siMeshSulciOperture      -G[rey]  <grey/white meshfilein>                
                         -L[CR]    <LCR/white meshfilein>	            
                         -m[odel]    <gyri model>			    
                         -l[evel]    <level model>		            
                         -s 		<sulci names>		            
                         [-n[bcc] <nb connected component> default=5]   
                         [--de <distance threshold  default=10 mm]    
                         [--dp <distance threshold  default=10 mm]    
                         -g[raph] <sulcus graph>                         
                         -[input] <mri volume>                          
                         -v[olume] <output thickness volume>                          
                         [-t[raduction] <traduction_file> default = traduction.txt]          
                         [-h[elp]]                                       
-------------------------------------------------------------------------
 Give different measures related to the sulci operture and cortex thickness    
-------------------------------------------------------------------------
     meshfilein          : input *.tri or *.mesh file                    
	gyri model          : Choice of the sulcus/sulcus relations         
     level model         : Choice of the level of description file *.def 
     sulci name          : Attribute for the name of the sulci in the graph (name or label) 
     sulcus graph        : Graph of the sulci *.arg                      
     traduction_file     : correspondance label string->short_label      
                           required by siParcellation.		    
     dmin                : max distance between the voxel and its projection
-------------------------------------------------------------------------

siMeshSulciProjection


-------------------------------------------------------------------------
siMeshSulciProjection    -i[nput] <meshfilein>                           
                         -m[odel]    <gyri model>			    
                         -l[evel]    <level model>		            
                         -s 		<sulci names>		            
                         -g[raph] <sulcus graph>                         
                         [-t[raduction] <traduction_file> default = traduction.txt]          
                         [-n[umbercc] <number_connex_components> default = 4]        
                         [-a[lpha_reg]    <estimation_ratio > default = 1]	    
                         [-e[min]     <euclidean distance threshold> default = 5 mm]  
                         [-p[min]     <plane distance threshold> default = 2 mm]  
                         [-V[olume_radius] <closing volume radius> default = 1.5 mm ]    
                         [-M[esh_radius] <closing radius for mesh > default = 1.5*r ]    
                         [-o[utput] <output_sulc_texture>]               
                         [--connexity <metric> default =mesh connexity
                         [-c[urvature] <curvature map>]                  
                         [-K          <curvature  coef.> default = 2]    
                         [-h[elp]]                                       
-------------------------------------------------------------------------
 Project sulcus bottom points (voxels) on mesh texture (nodes).          
 Only sulci present in the <gyri model> file  are projected.             
 Their label correspond to the hierarchy defined in the <level model> file
 There are two alternative approach for the projection.   
 The first one uses a metric combining an euclidean distance and map (curvature or depth,..) information. 
 The second one uses tangent plane.                                
-------------------------------------------------------------------------
     meshfilein          : input *.tri or *.mesh file                    
	gyri model          : Choice of the sulcus/sulcus relations         
     level model         : Choice of the level of description file *.def 
     sulci name          : Attribute for the name of the sulci in the graph (name or label) 
     sulcus graph        : Graph of the sulci *.arg                      
     traduction_file     : correspondance label string->short_label      
                           required by siParcellation.		    
     number_connex_components : minimal number of point in each connected component 
     estimation_ration   : Distance threshold for detecting outliers for affine projection estimation.
                           Only points closer than (estimation_ration * dmin) are used for the estimation
     dmin                : max distance between a voxel and its projection
     input_curvature     : input *.tex curvature                         
     curvature coef.: influence of the curvature          
	closing radius	    : Radius for the sulci closing in mm            
     output_sulc_texture : Projected sulci texture *.tex                 
     connexity           : Underlying mesh metric : euclidean/mesh connexity                 
-------------------------------------------------------------------------

siMkModelEdges

usage : 
bin/siMkModelEdges [-o num] modelGraph.arg labelsFile adapFile.mod foldgraphlist
bin/siMkModelEdges paramFile

-o num  : removes edges whose occurence frequency in the data is 
less or equal to num

siModelsErrorRateInfo.py

Usage: Compute mean/std/min/max of model errors (good, bad, mean) and could make an histogram.

Options:
  -h, --help            show this help message and exit
  -f FILTER, --labelsfilter=FILTER
                        only models matching this filter are covered.ex :
                        'label1,label2' or 'label' or 'regexp1,regexp2' (here
                        order is important)
  --filtermode=FILTER   strict, flexible or regexp
  --filter-fifty-percent
                        filter values equal to 0.5
  -m MODEL, --model=MODEL
                        model file name (default : model.arg)
  --hist=HIST           make histogram from classifiation/regression ratesof
                        models. HIST should be a format supported by pylab

siMonitor.py

Usage: Monitor sigraph learning process.

Options:
  -h, --help            show this help message and exit
  -f FILTER, --labelsfilter=FILTER
                        only models matching this filter are covered.ex :
                        'label1,label2' or 'label' or 'regexp1,regexp2' (here
                        order is important)
  --filtermode=FILTER   strict, flexible or regexp
  -m MODEL, --model=MODEL
                        model file name (default : model.arg)
  -n FILE, --newer=FILE
                        generated files must be newer than this file
  -t TASK, --task=TASK  monitoring task : models, log (default : models)
  --mode=MODE           monitoring mode : learning, generation, models
                        (default : learning)
  -o FILE, --outputbatch=FILE
                        batch file
  -r, --remote          enable remote control (default : disable)
  -l LOGFILENAME, --log=LOGFILENAME
                        analyzed log
  -i INPUTBATCH, --inputbatch=INPUTBATCH
                        input batch file

siMorpho


    siMorpho
    --------

Writes morphometry figures to disk files according to a model graph.
Each data graph is one single line on each file, and each file is a table for a
single element (sulcus or relation).
Elements to get figures on can be filtered by providing regular expressions or
a selection (newer mechanism)

Options :

[ -p <string> ]
    input parameters file (tree format) (richer than other parameter given on
    the commandline)
    Parameter file attributes:
    
    modelFile           string  !
    graphFiles          string  !
    labelsMapFile       string
    filter_attributes   string
    filter_pattern      string
    output_prefix       string
    verbose             int
    name_descriptors    int
    label_attribute     string
    descriptor_aliases  string
    print_labels        int
    subjects            string
    subject_regex       string
    selection           string

[ -m <string> ]
    model file

[ -g <vector of string> ]
    graphs to get morphometry figures on

[ -l <string> ]
    correspondance map from labels of the graph to learn to those used by the
    model

[ -o <string> ]
    append prefix to output data file names (followed with region models names)
    default: siMorpho_

[ --label_attribute <string> ]
    label attribute used to get labels from: usually "label" or "name", "auto"
    means try first label, and if no label is present, take name [default:auto]

[ --print-labels <S32> ]
    add labels/side column

[ --name-descriptors <S32> ]
    add header

[ --one-file <S32> ]
    one uniq output file (default: one file per sulci)

[ --filter-attributes <string> ]
    label, label1 label2, label label1 label2 (default)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


siMultilabelCompare


    siMultilabelCompare
    -------------------

Evaluation of different labelings.This command is a bit similar to siErrorStats
but allows to compare an arbitrary number of different labelings for the same
graph, and an arbitrary number of subjects

Options :

-o <string>
    output filename for stats

[ -i <vector of string> ]
    input graphs filenames and params. They should have the form
    filename.arg|subjectname|label_attribute|id_attribute, with:
    subjectname: identifier for the subject
    label_attribute: label or name
    id_attribute: attribute (int type) used to identify the same node on
    different copies of the same graph.
    If you are using a BrainVisa-like database, you can either use the -b
    option, or build the parameters list using a sed command of the form:
    ls */graphe/*.arg | sed -e \
    's%.*/\([^/]*\)/graphe/[^/]*\.arg%"\0|\1|label|index"%' \
    | awk '{ printf( "%s ", $0 )}'

[ -c <string> ]
    config file providing the list of graphs to compare. This file only
    contains a concatenation of the -i arguments equivaments.
    If you are using a BrainVisa-like database, you can either use the -b
    option, or build the config file using a sed command of the form:
    ls */graphe/*.arg | sed -e \
    's%.*/\([^/]*\)/graphe/[^/]*\.arg%\0|\1|label|index%' > configfile

[ -t <boolean> ]
    output as table (default is pyhton-like dictionary object)

[ -b <boolean> ]
    BrainVisa style: input parameters are only graph filenames which are
    organized as a BrainVisa database: <basepath>/subjectname/graphe/*.arg
    in this case, the label attribute is 'label' and the identifier attribute
    is 'index'.

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


siPIDcommand

usage : bin/siPIDcommand PIDfile command [params...]

execs command 'command' with given parameters and writes the process ID to file PIDfile

siParcellation


    siParcellation
    --------------

Compute parcellation in sulci regions and gyri. The input sulci texture must be
defined by siMeshSulciProjection

Options :

-i | --input <file name (read only): Mesh of VOID>
    grey/white mesh

-s | --sulci <file name (read only): texture of S16>
    input_texture: definition of the sulci texture (given by
    siMeshSulciProjection

-g | --graph <filename: Graph>
    output gyri graph

-m | --model <string>
    gyri model: Choice of the sulcus/sulcus relations ('gyri.gyr')

-o | --output <filename: texture of S16>
    output timetexture file (sulci and gyri texture): 0: sulci, 1 : sulci
    regions, 2: gyri, 3: gyri & sulci

[ -b | --brain <file name (read only): Mesh of VOID> ]
    brain mesh [used and required in 3D mode only]

[ -p | --parcelvol <filename: volume of S16> ]
    output gyri volume [used in 3D mode only]

[ -v | --value <S32> ]
    grey value in input_grey_white vol [default: 100]

[ -V | --Volume <file name (read only): volume of S16> ]
    input grey white volume [used and required in 3D mode only]

[ -T | --Time <U32> ]
    input sulci texture time [default: 0]

[ --sulcitranslation | --sulcitraduction <string> ]
    sulci translation file: correspondance label string->short_label
    [default:"sulcitraduction.txt"]

[ --gyritranslation | --gyritraduction <string> ]
    output gyri translation file: correspondance label string->short_label.
    This file will be written or completed if it already exists
    [default:"gyritraduction.txt"]

[ --connectivity | --connexity <boolean> ]
    use connectivity (true) or geodesic euclidean distance (false) [default:
    false]

[ --3D <boolean> ]
    compute 3D cortical ribbon gyrus graph [default: false]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


siPotentialSummary.py

Usage: Stores potential summary information into data graph nodes

Options:
  -h, --help            show this help message and exit
  -m MGRAPH, --model=MGRAPH
                        model graph filename
  -d DGRAPH, --data=DGRAPH
                        data graph filename

siPutTextureInModel


    siPutTextureInModel
    -------------------

no doc at the moment...

Options :

-m <string>
    model file

-v <string>
    value file

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


siRelax

siRelax
usage : 
bin/siRelax paramFile
bin/siRelax [-l labelsMapFile] [-n] [-u] [-t temp] [-m mode]
[-d rate] [-i tempICM] [-s stopRate] [-g gibbschange] [-v]
[-N nodesGrouping] [-p plotfile] [-u] [-L label] modelFile graphFile.arg

Labels a folds graph according to a model graph
by simulated annealing

Arguments : 

paramFile        :  parameters file for inputs for the command 
                    (Tree file)
-l labelsMapFile :  correspondance map from labels of the 
                    graph to learn to those used by the model
                    (default: sillons_modele.def)
-n               :  (nosave) do not save the graph after relaxation
-u               :  (uninitialized) do not initialize the fold
                    graph labels before annealing
-t temp          :  initial temperature of the relaxation
                    (default: 1.)
-m mode          :  annealing mode: metro, icm, gibbs
                    (default: gibbs)
-d rate          :  temperature decrease rate factor
                    (default: 0.95)
-i temp          :  temperature below which annealing switches
                    to ICM (default: 0., no ICM)
-s rate          :  stop rate: proportion of allowed changes
                    below which relaxation stops (default: 0.01)
-g gibbschange   :  number of synchronous changes allowed in
                    Gibbs and ICM modes (default: 2)
-N nodesGrouping :  nodes grouping while iterating on the graph:
                    VERTEX, CLIQUE (default: VERTEX)
-v               :  verbose mode
-p plotfile      :  saves the energies of each timestep in a 
                    file (useful for plotting)
-U               :  use 'unknown' label for initialization. The 
                    'unknown' label is set with the -L option
-L label         :  sets the default unknown label.
                    (default: 'unknown')

modelFile.arg  :  model graph file to train
graphFile.arg    :  graph to label

siRelax.py

Usage: Annealing to label sulci.

Options:
  -h, --help            show this help message and exit
  -c FILE, --config=FILE
                        siRelax config file
  -w MODE, --weight=MODE
                        mode to weight models (sulci and relations) : volume,
                        size, neighbours, volumeT, sizeT, neighboursT, ratio
                        (0 : only sulci, 1 : only relations, 0.5 :  classical
                        model), treshold (w < l => w = 0)
  -l FILE, --lambda=FILE
                        lambda parameter for ratio weights modifier :
                        (1-lambda) for sulci, (lambda) for relations. For
                        threshold modifier : truncate threshold.

siRevert


    siRevert
    --------

Reverts an overlearned model graph to its optimal state (saved during learning)

Options :

-m <string>
    model graph

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


siSulcalParcellation


-------------------------------------------------------------------------
siSulcalParcellation   -i[nput] <grey/white mesh>                                   
                  -s[sulci] <input_texture>                              
                  -g[raph] <output_gyri_graph>                           
                  -m[odel] <gyri model >                                 
                  -b[rain] <brain mesh >                                 
                  -o[utput] <output_gyri_texture>                          
                  -p[arcelfile] <output_gyri_volume>                        
                  [-v[alue] <grey value in input_grey_white vol>]                       
                  [-V[olume] <input_grey_white volume>]                       
                  [-T[ime] <input sulci texture time> default = 0]               
                  [-t[raduction] <traduction_file>  ] 
                   [--connexity ]                                       
                   [--3D ]                                       
                  [-h[elp]]                                              
-------------------------------------------------------------------------
 Compute parcellation in sulcal regions                           
 The input sulci texture must be defined by siMeshSulciProjection        
-------------------------------------------------------------------------
     meshfilein          : input *.tri or *.mesh file                    
     input_texture       : definition of the sulci texture (given by siMeshSulciProjection
	gyri model          : Choice of the sulcus/sulcus relations ('gyri.gyr')
     traduction_file     : correspondance label string->short_label      
                           required by siParcellation.		    
     connexity           : connexity or geodesic euclidean distance      
     3D                  : compute 3D cortical ribbon gyrus graph            
     output_vor_texture : output timetexture file (sulci and gyri texture)   
     0: sulci, 1 : sulcal regions
-------------------------------------------------------------------------

siSynthRelaxResult.py

Usage: Synthetize error rates results (default : if no option is passed : --mean is activated
siSynthRelaxResult.py [OPTIONS] file1.csv file2.csv...

Options:
  -h, --help            show this help message and exit
  -d TYPE, --database=TYPE
                        one among 2000, 2005, 2008 (default : 2008)
  --csv=FILE            store computed data in csv
  -m, --mean            Show mean values. Take the mean value of each subject
                        and then compute the mean over subjects
  -c, --correlation     Show correlations between errors and energy
  -b, --best            Show best values. Take the best value of each subject
                        and then compute the mean over subjects
  -s, --std             Show standard deviation mesures. Take the best/mean
                        (see -m option) value of each subject and then compute
                        the std over subjects
  -o, --old             old behaviour of siSynthRelaxResult.py

siTestModels


    siTestModels
    ------------

Tests some model configurations

Options :

-p <string>
    input parameters file (tree format) (richer than other parameter given on
    the commandline)
    Parameter file attributes:
    
    netFiles	string	!
    learnCfgFiles	string	!
    learnerFiles	string	!
    netTarget	string	!
    outputDir	string	!
    plotFields	string	!
    outPlotField	string	!
    errPlotField	string	!
    plotCmd		string

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


siTestModels.py

Usage: Test models on databases.

Options:
  -h, --help            show this help message and exit
  -f FILTER, --labelsfilter=FILTER
                        only models matching this filter are covered.ex :
                        'label1,label2' or 'label' or 'regexp1,regexp2' (here
                        order is important)
  --filtermode=FILTER   strict, flexible or regexp
  -m MODEL, --model=MODEL
                        model file name (default : model.arg)
  -t TEST, --test=TEST  model file name (default : model.arg). Only test
                        part of models databases(vectors shaped) is used by
                        default.
  --train               use train part of models databases
                        instead of test one.
  --hist=HIST           make histogram from classifiation/regression rates of
                        models. HIST should be a format supported by pylab

siTriangModel

usage : bin/siTriangModelmodel.arg folds.arg directory

siTryGauss

usage : bin/siTryGauss model.mod ncycles [c(ont)]

sigraph-config


    sigraph-config
    --------------

Get configuration info about SiGraph library and commands

Options :

[ --nomenclature <boolean> ]
    Print nomenclature path

[ --sishared <boolean> ]
    Print sigraph data/config path

[ --shfjshared <boolean> ]
    Print global SHFJ shared path

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


sulciCurvature.py

Usage: sulciCurvature.py [options]

calculate sulcuswise curvature maps and averages by sulcus

Options:
  -h, --help            show this help message and exit
  -i GRAPH, --input=GRAPH
                        labelled sulci graph
  -o CSVFILE, --output=CSVFILE
                        output CSV curvature stats file
  -m MESHDIR, --meshdir=MESHDIR
                        output directory for meshes and curvature textures
                        (default: don't write them)
  -c CURV, --curv=CURV  curvature calculation method: fem, barycenter, boix,
                        boixgaussian
  -l LABEL, --labelatt=LABEL
                        label attribute (label or name), default: guessed if
                        specified in graph, or take label
  -n, --nodewise        perform graph nodewise calculations, and possibly
                        output per-node meshes and curvatures if -m option is
                        also set
  -s SUBJECT, --subject=SUBJECT
                        subject name to write in CSV output. If not specified
                        it will not be written
  -f LABELSFILTER, --filter=LABELSFILTER
                        labels filter pattern (regular expression). Normally
                        labels are not filtered, all sulci are processed.
  -t TRANSLATION, --translation=TRANSLATION
                        labels translation: may be a .trl translation map, a
                        selection (.sel), or a nomenclature (.hie)
  --modeltrans=MODELTRANSLATION
                        model graph used for labels translation, used in
                        combination of the translation file, especially if the
                        latter is a nomenclature. Wen using aselection, the
                        model graph sould not be specified, and when using a
                        .trl translation, it is generally not so useful.
  -a, --append          append output to a possibly existing CSV file. The
                        output file will be locked using a <output>.lock
                        directory to avoid concurrent access by multiple
                        instances of sulciCurvature, and the CSV header will
                        be written only if the CSV file does not exist or is
                        empty.

sulciDistanceToLesion.py

Usage: sulciDistanceToLesion.py [options]

calculates a distance map from a lesion in the brain, and mean distance from
the lesion to all sulci. If the distance map is already calcualted, it can be
specified as input using the --indistance parameter, instead of the lesionfile
and brainfile.

Options:
  -h, --help            show this help message and exit
  -l LESIONFILE, --lesion=LESIONFILE
                        input lesion mask
  -L LGW, --lgreywhite=LGW
                        left grey/white mask
  -R RGW, --rgreywhite=RGW
                        right grey/white mask
  --lsk=LSK             left sulci skeleton (optional) used to avoid crossing
                        sulci
  --rsk=RSK             right sulci skeleton (optional) used to avoid crossing
                        sulci
  -o OUTPUTCSV, --output=OUTPUTCSV
                        output CSV file
  -g GRAPHS, --graph=GRAPHS
                        sulci graph files, several can be specified (generally
                        left and right hemispheres)
  --indistance=INDISTFILE
                        input distance map image, recalculated if not
                        specified
  -d DISTFILE, --distance=DISTFILE
                        output distance map image, not written if not
                        specified
  --labelatt=LABEL      label attribute (label or name), default: guessed if
                        specified in graphs, or take label
  -s SUBJECT, --subject=SUBJECT
                        subject name to write in CSV output. If not specified
                        it will not be written
  -t TRANSLATION, --translation=TRANSLATION
                        labels translation: may be a .trl translation map, a
                        selection (.sel), or a nomenclature (.hie)
  --modeltrans=MODELTRANSLATION
                        model graph used for labels translation, used in
                        combination of the translation file, especially if the
                        latter is a nomenclature. Wen using aselection, the
                        model graph sould not be specified, and when using a
                        .trl translation, it is generally not so useful.

sulciDistanceToNeighbours.py

Usage: sulciDistanceToNeighbours.py [options]

calculate sulcuswise distance to other neighbouring sulci

Options:
  -h, --help            show this help message and exit
  -i GRAPH, --input=GRAPH
                        labelled sulci graph
  -o CSVFILE, --output=CSVFILE
                        output CSV curvature stats file
  -l LABEL, --labelatt=LABEL
                        label attribute (label or name), default: guessed if
                        specified in graph, or take label
  -s SUBJECT, --subject=SUBJECT
                        subject name to write in CSV output. If not specified
                        it will not be written
  -f LABELSFILTER, --filter=LABELSFILTER
                        labels filter pattern (regular expression). Normally
                        labels are not filtered, all sulci are processed.
  -t TRANSLATION, --translation=TRANSLATION
                        labels translation: may be a .trl translation map, a
                        selection (.sel), or a nomenclature (.hie)
  --modeltrans=MODELTRANSLATION
                        model graph used for labels translation, used in
                        combination of the translation file, especially if the
                        latter is a nomenclature. Wen using aselection, the
                        model graph sould not be specified, and when using a
                        .trl translation, it is generally not so useful.

sulciLabelConsistencyCheck.py

Usage: sulciLabelConsistencyCheck.py [options]

Consistency check for sulci graph labels: typically, ensure there is no
hemisphere mismatch (left label in right hemisphere).

Options:
  -h, --help            show this help message and exit
  -i GRAPH, --input=GRAPH
                        labelled sulci graph
  -l LABEL, --labelatt=LABEL
                        label attribute (label or name), default: guessed if
                        specified in graph, or take name
  -s SIDE, --side=SIDE  side (left or right)

sulciReplaceDescriptors.py

Usage: sulciReplaceDescriptors.py [options]

Replace the CliqueDescriptor in a model graph to another one

Options:
  -h, --help            show this help message and exit
  -i MGRAPH, --input=MGRAPH
                        input model graph
  -o OUTMGRAPH, --output=OUTMGRAPH
                        output model graph
  -n NODEMODEL, --nodemodel=NODEMODEL
                        model element to set into the model graph nodes
  -r RELMODEL, --relmodel=RELMODEL
                        model element to set into the model graph nodes

sulciSulcuswisePotentials.py

Usage: sulciSulcuswisePotentials.py [options]

Records sulcuswise potential (including relations) in a CSV file

Options:
  -h, --help            show this help message and exit
  -o OUTPUT, --output=OUTPUT
                        output CSV file
  -m MODEL, --model=MODEL
                        model graph
  -i GRAPHS, --input=GRAPHS
                        input graph(s). Several graphs may be specified

morphologist

qt backend: PyQt5
Usage: morphologist [options]

Options:
  -h, --help            show this help message and exit
  -s STUDY_DIRECTORY, --study=STUDY_DIRECTORY
                        Opens the interface with the study loaded.
  -i IMPORT_STUDY_DIRECTORY, --import=IMPORT_STUDY_DIRECTORY
                        Opens the interface with a new study loaded, based on
                        an imported brainvisa directory.

  Neurospin specific options:
    --brainomics        Images can be imported in a study from Brainomics
                        Cubicweb database

  Debug options:
    --mock              Test mode, runs mock intra analysis

AimsAdaptiveSelVoxel


    AimsAdaptiveSelVoxel
    --------------------

Create an image of selected voxels

Options :

-i <string>
    input file Image

[ -c <S32> ]
    Channel of multi-channel image
    Possible types and values:
    type : RGB or RGBA
    values: 0=red, 1=green, 2=blue, 3=alpha, 4=norm
    
    type : HSV
    values: 0=hue, 1=saturation, 2=value, 4=norm
    
    [default is set to norm]
    

--grd <string>
    input file gradient norm

-o <string>
    output file

[ -ob <string> ]
    output Bucket Of Void file

[ -obv <string> ]
    output Bucket Of S16 file, containing matching values

[ --tIma <S16> ]
    threshold IMAGE <seuil %  Short >

[ --tGrd <S16> ]
    threshold GRADIENT <seuil %  Short >

[ --psg <FLOAT> ]
    Prob 'without' gradient <float>

[ --pagMin <FLOAT> ]
    Prob 'with' gradient MIN float

[ --pagMax <FLOAT> ]
    Prob 'with' gradient MAX float

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsAxialProjection


    AimsAxialProjection
    -------------------

Colliculi parameters projection

Options :

[ -i <file name (read only): volume of S16> ]
    input image

[ -m <file name (read only): volume of S16> ]
    mask image

[ -o <filename: volume of DOUBLE> ]
    output image

[ -p <string> ]
    output parameters (ASCII)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsBorderGenerate


    AimsBorderGenerate
    ------------------

Generate border around image

Options :

-i <string>
    input data

[ -m <string> ]
    mask for data

[ -bx <FLOAT> ]
    border size (in mm) for x dimension

[ -by <FLOAT> ]
    border size (in mm) for y dimension

[ -bz <FLOAT> ]
    border size (in mm) for z dimension

[ -bv <string> ]
    border value to use

[ -u <boolean> ]
    use background instead of border when it is possible

[ -hxyz <boolean> ]
    homogenize x, y and z borders using the maximum border size

[ -om <string> ]
    output motion

-o <string>
    output image

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsBorderInfo


    AimsBorderInfo
    --------------

Border info

Options :

-i <string>
    Input image

[ -b <VECTOR_OF_3_S16> ]
    Border width, default : (10 ,10 ,10)

[ -t <string> ]
    Smoothing filter type: mea[n], med[ian], min[imum], max[imum], maj[ority]
    (default = median)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsCenterSlices


    AimsCenterSlices
    ----------------

Command that stacks images and uses gravity centers to coalign images

Options :

-i <list of string>
    input files (1 minimum)

[ -dx <S32> ]
    dx dimension [Default: input]

[ -dy <S32> ]
    dy dimension [Default: input]

[ -z <FLOAT> ]
    z thickness [Default: input]

[ -resol <FLOAT> ]
    scan resolution [Default: input voxelsize]

[ -rx <FLOAT> ]
    scan resolution for X [Default: input X voxelsize]

[ -ry <FLOAT> ]
    scan resolution for Y [Default: input Y voxelsize]

[ -vs <string> ]
    voxel size unit (mm or dpi) [Default: dpi]

[ -usegc <boolean> ]
    uses gravity center to center slices [Default: true]

[ -ratio <FLOAT> ]
    seuil = % max [default 0.15 = 15%]

[ -v <string> ]
    values of interest high/low [Default=low]

-o <string>
    output image

[ -t <string> ]
    output translations list [default=not written]

[ -m <string> ]
    output motion base name [default=not written]

[ -c <U8> ]
    Channel to use to process multi-channel image
    Possible types and values:
    type : RGB or RGBA
    values: 0=red, 1=green, 2=blue, 4=norm
    
    type : HSV
    values: 0=hue, 1=saturation, 2=value, 4=norm
    

[ -d <string> ]
    Default value for borders [default=0]
    

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsFovAdapt


    AimsFovAdapt
    ------------

Adapt FOV of a volume according to reference volume FOV

Options :

[ -i <file name (read only): { Volume of DOUBLE, Volume of FLOAT, Volume of RGB,
    Volume of RGBA, Volume of S16, Volume of S32, Volume of S8, Volume of U16,
    Volume of U32, Volume of U8 }>  Input image to be cropped ]

[ -r <file name (read only): { Volume of DOUBLE, Volume of FLOAT, Volume of RGB,
    Volume of RGBA, Volume of S16, Volume of S32, Volume of S8, Volume of U16,
    Volume of U32, Volume of U8 }>  Input image Reference ]

[ -bv <string> ]
    border value to use

[ -o <string> ]
    Output image cropped

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsGL2Activity

inv_log10 = 0.434294

    AimsGL2Activity
    ---------------

Convert a grey level image to an activity image

Options :

-i <string>
    input grey level image

-o <string>
    output activity image

[ -p <string> ]
    output polynom image

[ -d <S32> ]
    polynome degree for fit (default = 4)

[ -s <S32> ]
    1 = use classic standards, 0 = indicate your standards (default = 1)

[ -c <S32> ]
    1 = conversion niveaux de gris en D.O, 0 = non conversion (default = 1)

[ -gl <string> ]
    input grey level standard data

[ -act <string> ]
    input activity standard data

[ -input <S32> ]
    specify command line input for grey level and activity is enabled (default
    = 1)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsIndividStackSlices


    AimsIndividStackSlices
    ----------------------

Individualize and stack slices from multiple scan

Options :

-i <string>
    Input original image

[ -pi <string> ]
    Input preprocessed image

-n <S32>
    Number of slices

[ --dimsizes <vector of S32> ]
    Dimensions sizes

[ --dimorders <vector of S32> ]
    Dimensions orders

-z <FLOAT>
    Inter slice space (in mm)

-res <S32>
    Scan resolution (in dpi)

[ -dx <S32> ]
    X dimension of the final volume

[ -dy <S32> ]
    Y dimension of the final volume

[ -lt <S32> ]
    Lower threshold [manual activation]

[ -ht <S32> ]
    Higher threshold [manual activation]

-ms <S32>
    Minimal surface of slices [in mm2]

[ -o <string> ]
    Output labelled image

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsInterSliceNormalize


    AimsInterSliceNormalize
    -----------------------

Normalize the intensity through 3D volume.
This process first computes a reference value for the intensity's mean and
variance. The reference slice may be a given slice of the input volume, or a
given slice of a reference volume if one is passed.
The intensity's mean and variance are then computed in each slice of the
estimate volume (the input volume if none is given), and linear coefficients A
and B are computed so that A * EST_SIGNAL + B has the same mean and variance as
REF_SIGNAL.
The transformation is finally applied to the input volume and returned in the
output volume.
If masks are provided, only the signal in the masks is used for estimation.
However, the transformation is applied to the entire volume.

Options :

-i | --input <string>
    input data to use to process intensity mean and variance

[ -j | --input-estimate <string> ]
    input data to use to estimate mean and variance [default : uses the input
    data]

[ -k | --input-reference <string> ]
    input data to use as reference [default: uses estimate or else input data]

-o | --output <string>
    output data

[ -m | --input-mask-estimate <string> ]
    input mask for processed/estimate images

[ -n | --input-mask-reference <string> ]
    input mask for reference image

[ -p <string> ]
    input mask for estimate image

[ -s <S32> ]
    reference slice [default: 0]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel | -d <S32> ]
    Set debug information level (default = 0)

[ --verbose | -v [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsManualRegistration


----------------------------------------------------------------
AimsManualRegistration                                          
            -f[rom]     < .arg file >                           
            -t[o]       < .arg file >                           
            -o[utput]   < displacement file: from_TO_to.trm >   
            --l[oose]    < loose or point to point registration>
            --transfo  < 1=rigide, 2=simi, 3=affine (default=1)>
           [-h[elp]]                                            
----------------------------------------------------------------
 Compute manual registration					   
 Both arg files can be filled with anatomist roi module, but must
 - contain only one point per region				   
 - region must be correctly ordered : same roi_label or order   
   of creation for appariated points in both graphs		   
----------------------------------------------------------------
   .arg file: voi type file					   
   --loose condition: registration with two points plus a point 
                  defining a plane (inter-hemispheric plane)    
----------------------------------------------------------------

AimsMidPlaneAlign


    AimsMidPlaneAlign
    -----------------

Rectify the image and compute the rectified transformation (superposition of
the interhemispheric plane with the plane x=dimX/2)

Options :

-i <string>
    input image to rectify

[ -c <S32> ]
    Channel of multi-channel image to use during transformation estimation
    Possible types and values:
    type : RGB or RGBA
    values: 0=red, 1=green, 2=blue, 3=alpha, 4=norm
    
    type : HSV
    values: 0=hue, 1=saturation, 2=value, 4=norm
    
    [default is set to norm]
    

[ -o <string> ]
    output rectified image (default=rectified)

[ -m <string> ]
    output motion (default=input_TO_output.trm)

[ -g <boolean> ]
    generate output motion (default=true)

[ -p <string> ]
    output interhemispheric plane equation (default=not written)

[ --start <S32> ]
    pyramid start level for registration

[ --stop <S32> ]
    pyramid stop level for registration

[ -bv <string> ]
    Background value to use

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsReadDpy


    AimsReadDpy
    -----------

Read amyloid plaques data

Options :

-i <string>
    input data filename

[ -o <string> ]
    output label data filename

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


bioModelClassify


    bioModelClassify
    ----------------

Classify image using multi variate gaussian model.
Each pixel to classify is processed as a measure vectors (R, G, B, M) or (H, S,
V, M), where M is the mean value of voxels in the neighborhood (depending on
the connexity). Once measure vectors are processed, density of probability are
processed for each class in the model. The maximum probability of a measure
vector to belong to a class determine the class of the voxel.
(cf. bioVision algorithm)

Options :

-i <string>
    Input image

-bv <string>
    Input classes file

[ -o <string> ]
    Output image

[ -m <string> ]
    Input mask file

[ -p <string> ]
    Output probabilities image

[ -e <string> ]
    Output density image

[ -om <string> ]
    Output neighborhood measure image

[ -wb <boolean> ]
    If reading is done with borders, you can set this to true to give up
    testing for borders when computing measure vectors.

[ -l <vector of S32> ]
    Output labels to use for the resulting segmentation

[ -c <vector of string> ]
    Output classes order to use for the resulting segmentation

[ -tc <vector of S32> ]
    Tested coordinates (only display probabilities for this coordinates)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel | -d <S32> ]
    Set debug information level (default = 0)

[ --verbose | -v [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


bioModelGenerate


    bioModelGenerate
    ----------------

Learn multi variate gaussian models using segmented images.
For each segmented pixel measure vectors are processed as (R, G, B, M)
or (H, S, V, M), where M is the mean value of voxels in the neighborhood
(depending on the connexity)
Once measure vectors are processed, clusters are determined to approximate
multi variate gaussian model.
(cf. bioVision algorithm)

Options :

-i <list of string>
    Input image(s)

-g <list of string>
    ROI Graph(s). ROI are used to determine the class of each segmented voxel

-bv <string>
    Output bioVision classes file

[ -pm <string> ]
    Pixel measure used [default : rgbm]

[ -om <string> ]
    Output neighborhood measure image

[ -d <S32> ]
    Neighborhood direction (1 : diagonal, 2 : 4-connex, 3 : disk) [default : 1]

[ -a <DOUBLE> ]
    Neighborhood amplitude [default : 4]

[ -l <boolean> ]
    Neighborhood in the plan or in the volume [default : true]

[ -u <boolean> ]
    Neighborhood includes the voxel himself [default : false]

[ -t <DOUBLE> ]
    Clustering threshold [default : 1.0]

[ -s <DOUBLE> ]
    Clustering minimal temperature [default : 2]

[ -r <DOUBLE> ]
    Clustering sigma ratio used to divide sigma [default : 2]

[ -n <S32> ]
    Clustering maximum number of clusters [default : 12]

[ -ms <DOUBLE> ]
    Cluster minimum size (percent of class voxel size) [default : 0.0]

[ -cp <S32> ]
    Cluster creation policy (1 : histogram maxima, 2 : median) [default : 1]

[ -p <list of DOUBLE> ]
    Probability prior for each class [default : 1 / number of classes]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose | -v [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


bioReadDpy


    bioReadDpy
    ----------

Read biovision classes data

Options :

-i <string>
    input  data filename

[ -g <boolean> ]
    generate histograms for vector measures

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsAffineRegister


    AimsAffineRegister
    ------------------

Registration according to Mutual Information Method

Options :

[ -f <vector of string> ]
    freedom degrees (Tx, Ty, Tz, Rx, Ry, Rz, Sx, Sy, Sz, Cx, Cy, Cz)

[ -r <string> ]
    source S16 reference data

[ -t <string> ]
    source S16 test data (to register)

[ -o <string> ]
    destination S16 data

[ -l <string> ]
    logger

[ --Tx <FLOAT> ]
    init Translation coord 

[ --Ty <FLOAT> ]
    init Translation coord 

[ --Tz <FLOAT> ]
    init Translation coord 

[ --Rx <FLOAT> ]
    init Rotation coord 

[ --Ry <FLOAT> ]
    init Rotation coord 

[ --Rz <FLOAT> ]
    init Rotation coord 

[ --Sx <FLOAT> ]
    init Scaling coord 

[ --Sy <FLOAT> ]
    init Scaling coord 

[ --Sz <FLOAT> ]
    init Scaling coord 

[ --Cx <FLOAT> ]
    init Shear coord 

[ --Cy <FLOAT> ]
    init Shear coord 

[ --Cz <FLOAT> ]
    init Shear coord 

[ --dTx <FLOAT> ]
    increment for variable Tx

[ --dTy <FLOAT> ]
    increment for variable Ty

[ --dTz <FLOAT> ]
    increment for variable Tz

[ --dRx <FLOAT> ]
    increment for variable Rx

[ --dRy <FLOAT> ]
    increment for variable Ry

[ --dRz <FLOAT> ]
    increment for variable Rz

[ --dSx <FLOAT> ]
    increment for variable Sx

[ --dSy <FLOAT> ]
    increment for variable Sy

[ --dSz <FLOAT> ]
    increment for variable Sz

[ --dCx <FLOAT> ]
    increment for variable Cx

[ --dCy <FLOAT> ]
    increment for variable Cy

[ --dCz <FLOAT> ]
    increment for variable Cz

[ --dir <string> ]
    output filename for direct transform parameter

[ --inv <string> ]
    output filename for inverse transform parameter

[ --interpolation <string> ]
    interpolation  nearest/linear/spline [default=linear]

[ --optimizer <string> ]
    optimizer  powell/random/single [default=powell]

[ --pdfcalc <string> ]
    pdf calculus mode  direct/pv [default=direct]

[ --gcinit <string> ]
    init with GravCenter yes/no [default=yes]

[ --index <string> ]
    index to be optimized mi/cr [default=mi]

[ --refstartpyr <S64> ]
    start resolution level of the multiresolution optimization for ref

[ --refendpyr <S64> ]
    end resolution level of the multiresolution optimization for ref

[ --teststartpyr <S64> ]
    start resolution level of the multiresolution optimization for test

[ --testendpyr <S64> ]
    end resolution level of the multiresolution optimization for test

[ --serialnum <S64> ]
    number of the frame to consider for ref 

[ --pays_size <S64> ]
    half size the volume generated if algo=other activated 

[ --graylevel <S64> ]
    numb of classes in histogram pdf estimation [def.=64]

[ --masksize <S64> ]
    size of the gaussian convolution mask in pdf estimation for Mutual
    Information [default=5]

[ --error <FLOAT> ]
    tolerance on results [default=0.00001]

[ --seuiltest <FLOAT> ]
    relative thresh applied prior to grav cent estimation

[ --seuilref <FLOAT> ]
    relative thresh applied prior to grav cent estimation

[ --verbosity <S64> ]
    verbose level

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsAmyloidDensity


    AimsAmyloidDensity
    ------------------

Interpolation of plaques

Options :

-i <file name (read only): volume of S16>
    Input proba plaques image

-m <file name (read only): volume of S16>
    Input Binary Mask

[ -r <DOUBLE> ]
    Radius of STRUCT ELEMT

-o <filename: volume of DOUBLE>
    Output image

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsAmyloidDetection


    AimsAmyloidDetection
    --------------------

Detection of plaques

Options :

-i <file name (read only): volume of RGB>
    Input RGB image

-o <filename: volume of RGB>
    Output RGB proba image

-d <filename: N3bio7DpyDataE>
    Output features data file

[ -s <S32> ]
    Shape paremeter [Default=10]

[ -a <FLOAT> ]
    Maximal area [Default=0.05]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsAmyloidFiltering


    AimsAmyloidFiltering
    --------------------

Filtering Amyloid Plaques detected

Options :

-rgb <file name (read only): volume of RGB>
    Input original RGB image

-bin <file name (read only): volume of S16>
    Input detected AP binary image

-mask <file name (read only): volume of S16>
    Input tissue mask binary image

[ -ms <S32> ]
    Mimimal AP size [Defaut: 2]

[ -Ms <S32> ]
    Maximal AP size [Default: 1000]

[ -a <FLOAT> ]
    Maximal anisotropy accepted [Default: 3]

-d <filename: N3bio7DpyDataE>
    Output AP final DPY file

-o <filename: volume of S16>
    Output AP final image

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsAmyloidLoadAvgDistNeigh


    AimsAmyloidLoadAvgDistNeigh
    ---------------------------

Interpolation of plaques

Options :

[ -i <file name (read only): volume of S16> ]
    Input proba plaques image

[ -m <file name (read only): volume of S16> ]
    Input Binary Mask

[ -o <filename: volume of DOUBLE> ]
    Output image

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsAmyloidLoadInvSurfVor


    AimsAmyloidLoadInvSurfVor
    -------------------------

Interpolation of plaques

Options :

[ -i <file name (read only): volume of S16> ]
    Input proba plaques image

[ -m <file name (read only): volume of S16> ]
    Input Binary Mask

[ -o <filename: volume of DOUBLE> ]
    Output image

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsAmyloidMRIDetection


    AimsAmyloidMRIDetection
    -----------------------

Detection of plaques

Options :

[ -i <file name (read only): volume of RGB> ]
    Input RGB image

[ -o <filename: volume of RGB> ]
    Output RGB proba image

[ -d <string> ]
    Output features data file

[ -s <S32> ]
    Shape paremeter [Default=10]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsAreaNbConnectCompRatio


    AimsAreaNbConnectCompRatio
    --------------------------

Evolution of the Area/Nb connected comp Ratio

Options :

-i <file name (read only): volume of FLOAT>
    Input image

[ -m <file name (read only): volume of FLOAT> ]
    mask image

[ -n <S32> ]
    number of bins [default : 255]

[ -r <string> ]
    Text output

-d <filename: volume of FLOAT>
    Data array output

-o <filename: volume of FLOAT>
    Thresholded image

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsBinaryBorder


    AimsBinaryBorder
    ----------------

Binary border computing

Options :

-i <file name (read only): volume of U8>
    Input grey-level image

[ -c <U8> ]
    Connexity 4 or 8 [default : 4]

-o <filename: volume of U8>
    Output image

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsBinaryBoundingBox


    AimsBinaryBoundingBox
    ---------------------

Extract bounding box of an object from the binary image 

Options :

-i <string>
    input binary data

-o <string>
    output minf file. It contains the bounding box parameters [bx, by, bX, bY]
    for each slice

[ -c <FLOAT> ]
    constraint validation for the bounding box parameters, [default in percent
    : 0.0]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsBorderCrop


    AimsBorderCrop
    --------------

Border croping

Options :

-i <file name (read only): volume of RGB>
    Input RGB image

[ -b <U8> ]
    Border_value, default : 255 (white)]

-o <filename: volume of RGB>
    Output image

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsBorderLineProj


    AimsBorderLineProj
    ------------------

Compute direct assess to image border

Options :

-i <file name (read only): volume of S16>
    Input image

[ -o <string> ]
    Output projection image [Default: extension *.proj added]

[ -od <string> ]
    Output distance image [Default: extension *.dist added]

-bv <S16>
    Background value

[ -m <string> ]
    Mask image [Compute value if mask!=0]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsBoundingBoxCalculation


    AimsBoundingBoxCalculation
    --------------------------

calculate the bounding box parameters from the labeled volume

Options :

-i <string>
    input labeled volume

-o <string>
    output bounding box (minf file)

[ -bx <FLOAT> ]
    border size for x direction (in mm) [default : 0mm]

[ -by <FLOAT> ]
    border size for y direction (in mm) [default : 0mm]

[ -z <S32> ]
    first z coordinate [default : 0]

[ -Z <S32> ]
    last z coordinate [default : sizeZ-1]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsBoundingBoxExtraction


    AimsBoundingBoxExtraction
    -------------------------

Get the grid extraction from the labeled volume and voronoi's diagram

Options :

-i <string>
    input labeled volume

-s <string>
    input voronoi volume

-o <string>
    output minf file

[ -p <FLOAT> ]
    Constraint validation for the grid parameters [default in percent : 0.0 =>
    1 voxel of neighbor label found]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsChannelProcess


    AimsChannelProcess
    ------------------

Process an image using channels.
Each pixel is processed as a measure vectors (R, G, B, M)
or (H, S, V, M), where M is the mean value of voxels in the neighborhood
(depending on the connexity)

Options :

-i <string>
    Input image

-o <string>
    Output image

[ -m <string> ]
    Input mask file

[ --ip <string> ]
    Image processor to use (r, g, b, m, h, s, v) [default : m]

[ --melement <S32> ]
    Specify M element type (1: diagonal cross, 2: cross, 3: disk) [default : 3]

[ --mamplitude <DOUBLE> ]
    Specify M element size (in voxels) [default : 1]

[ --mplanar <boolean> ]
    Specify M is processed in axial plan (true) or in 3D (false) [default :
    true]

[ --musecenter <boolean> ]
    Specify M uses central voxel or not [default : false].

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel | -d <S32> ]
    Set debug information level (default = 0)

[ --verbose | -v [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsComponentFeatures


    AimsComponentFeatures
    ---------------------

Components features computing

Options :

-i <file name (read only): volume of S32>
    Input labelized image to read

-vo <file name (read only): volume of S32>
    Voronoi image to read

-col <file name (read only): volume of RGB>
    Input colored image

[ -o <filename: volume of FLOAT> ]
    Output parameterized Image

[ -vs <filename: volume of FLOAT> ]
    Visualization Image

[ -c <filename: volume of FLOAT> ]
    Contribution Image

[ -d <filename: volume of FLOAT> ]
    Dilation Feature in Voronoi Image

[ -p <filename: 21ParameterizedAimsDataIdE> ]
    Output parameters image

[ -k <S32> ]
    
    default value: 1
    
    step for computing feret diameter: it defines the number of directions for
    projections and its value must be specified in degree (only between 0 and
    45 degrees)

[ -vis <string> ]
    ----list of parameters for visualization ----
    default value: component_bb
    
    comparison: between components according to a choosen parameter
    component_bb
    edges_N4
    edges_N8
    extrema_neighbor:   farest and nearest neighbor from the given component 
    mass_center
    neighborhood
    voronoi_bb
    
    ----list of parameters for parameterizing ----
    circularity
    feret_diameter_max: maximum projection to many directions
    feret_diameter_min: minimum projection
    isotropy
    label_area_mm2
    label_area_px
    mean_r
    orientation: angle between the inertia axis and the normal abscissa axis
    orientation_angle
    perimeter_n4
    perimeter_n8
    perimeter_n4_n8
    hsv_mean_hue
    hsv_mean_saturation
    hsv_mean_value
    hsv_stand_dev_hue
    hsv_stand_dev_saturation
    hsv_stand_dev_value
    rgb_mean_red
    rgb_mean_green
    rgb_mean_blue
    rgb_stand_dev_red
    rgb_stand_dev_green
    rgb_stand_dev_blue
    stand_dev_r
    thinness
    voronoi_area_px
    voronoi_area_mm2

[ -l <S32> ]
    default value: maximum of InputImage 
    
    more information about this label

[ -comp <string> ]
    ---------------comparison---------------
    list of parameters you could use to make comparison between components: 
    it is necessary to precise this only if you choose comparison for
    visualization
    default value: perimeter_N4-N8
    
    perimeter_N4
    perimeter_N8
    perimeter_N4-N8
    component_area_px
    component_area_mm
    vor_area_px
    vor_area_mm
    thinness
    isotropy
    circularity
    mean_radius
    stand_dev_radius
    feret_diameter_max
    feret_diameter_min

[ -m <string> ]
    mode used to generate output image.
    Available modes are :
    'component' => set parameter value on each voxel of components
    'gravity_center' => set parameter value only to gravity center voxel of
    components
    'contribution' => only considers the part of the component in the new
    pixel[default: 'gravity_center']

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsComponentFeaturesMapGenerate


    AimsComponentFeaturesMapGenerate
    --------------------------------

Components features parametric map

According to 2 basic images (labelled image, parameters image), generate a
parametric map of a selected feature of the components.

Options :

[ -lab <file name (read only): volume of S32> ]
    Input labelled image of the components
    if -m is gravity_center, this input is not needed
    if -m is contribution, this input is necessary

-par <file name (read only): 21ParameterizedAimsDataIdE>
    Input 2D parameters image

-map <filename: volume of DOUBLE>
    Output generated feature map

[ -rx <S32> ]
    X number of voxels to aggregate [default = 1]

[ -ry <S32> ]
    Y number of voxels to aggregate [default = 1]

[ -rz <S32> ]
    Z number of voxels to aggregate [default = 1]

[ -f <string> ]
    Select a feature to generate its parametric map
    
    --------------------- list of features ---------------------
    
    counting           	:	 counting number of components
    				 work only with mode gravity_center
    area_px            	:	 area of each component (unit: px²)
    area_mm2           	:	 area of each component (unit: mm²)
    perimeter_n4       	:	 perimeter of each component based on
    				 4-connected(unit: px)
    perimeter_n8       	:	 perimeter of each component based on
    				 8-connected(unit: px)
    perimeter_n4_n8    	:	 (perimeter_n4*0.414+perimeter_n8*0.586)/1.055
    				 (unit: px)
    angle              	:	 angle between the inertia axis and the normal
    				 abscissa axis
    circularity        	:	 4*pi*area/perimeter_n4_n8²
    thinness           	:	 perimeter_n4_n8/area
    isotropy           	:	 feret_diameter_min/feret_diameter_max
    mean_radius        	:	 mean radius
    stand_dev_radius   	:	 standard deviation of radius
    radius_variation   	:	 sum((r(i)-r(i+1))²)/n 
    				 i is a radius of the component, i+1 its adjacent radius
    				 n is the total number of radius of each component
    color_h_mean       	:	 mean value of hue
    color_s_mean       	:	 mean value of saturation
    color_v_mean       	:	 mean value of value (lightness)
    color_h_stand_dev  	:	 standard deviation of hue
    color_s_stand_dev  	:	 standard deviation of saturation
    color_v_stand_dev  	:	 standard deviation of value (lightness)
    color_r_mean       	:	 mean value of red
    color_g_mean       	:	 mean value of blue
    color_b_mean       	:	 mean value of green
    color_r_stand_dev  	:	 standard deviation of red
    color_g_stand_dev  	:	 standard deviation of blue
    color_b_stand_dev  	:	 standard deviation of green
    voronoi_area_px    	:	 area of voronoi of components (unit: px²)
    voronoi_area_mm2   	:	 area of voronoi of components (unit: mm²)
    
    [default value: area_px]

[ -m <string> ]
    mode used to generate the parametric map
    
    --------------------- list of modes ---------------------
    
    gravity_center 	:	 attribute feature value only to the gravity center
    				 voxel of components
    contribution   	:	 consider the edge effect, apply a weight to each pixel
    				 based on its contribution
    [default: gravity_center]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsComponentFeaturesProcess


    AimsComponentFeaturesProcess
    ----------------------------

Components features computing

According to 3 basic images (color image, labelled image, voronoi image), 
calculate all components features, for example, area, perimeter, mass center,
circularity, thinness, isotropy, mean radius, color parameters, and so on.
Totally 47 features are saved in a parameters image

Options :

-col <file name (read only): volume of RGB>
    Input original color image

-lab <file name (read only): volume of S32>
    Input labelled image of the components

-vor <file name (read only): volume of S32>
    Input voronoi image of the components

-par <filename: 21ParameterizedAimsDataIdE>
    Output 2D parameters image
    X: component label
    T: parameter

[ -k <S32> ]
    parameter to compute feret diameter
    It turns the object step by step, after every rotation, it calculates the
    projection of object in both x and y direction. The maximum/minimum
    projection is the maximum/minimum feret diameter.
    This option defines the pace for each rotation and its value must be
    specified in degree (only between 1 and 45 degrees).
    [default = 1]

[ -l <S32> ]
    choice of label (from 1 to the total number of components)
    choose a label to study more information about its neighbors, calculate
    euclidian distance between this label and its neighbors.
    [default value: maximum label of components] 

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsComponentFeaturesVisualize


    AimsComponentFeaturesVisualize
    ------------------------------

Components features visualization

According to labelled image, parameters image and possibly voronoi image,
visualize a certain feature.

Options :

-lab <file name (read only): volume of S32>
    Input labelled image of the components

[ -vor <file name (read only): volume of S32> ]
    Input optional voronoi image of the components
    If attribute a feature value to the entire corresponding voronoi region,
    this input is necessary, and option -t should be set true.

-par <file name (read only): 21ParameterizedAimsDataIdE>
    Input 2D parameters image

-vis <filename: volume of DOUBLE>
    Output visualized image

[ -t <boolean> ]
    Attribute the value of a feature of components to the entire corresponding
    voronoi region
    If true, generate an image in which the feature is expanded in voronoi zone,
    voronoi image is necessary.
    [default value: false]

[ -f <string> ]
    Select a feature to visualize
    
    ------------- list of features for visualization -------------
    
    boundingbox         	:	 the smallest box within which all the points of
    					 a component lie
    edge_n4             	:	 edge of each component based on 4-connected
    edge_n8             	:	 edge of each component based on 8-connected
    edge_n4_order       	:	 edge of each component in order based on
    					 4-connected
    edge_n8_order       	:	 edge of each component in order based on
    					 8-connected
    mass_center         	:	 mass center of each component
    boundingbox_voronoi 	:	 the smallest box within which all the points of
    					 voronoi of a component lie
    area_px             	:	 area of each component (unit: px²)
    area_mm2            	:	 area of each component (unit: mm²)
    perimeter_n4        	:	 perimeter of each component based on
    					 4-connected(unit: px)
    perimeter_n8        	:	 perimeter of each component based on
    					 8-connected(unit: px)
    perimeter_n4_n8     	:	 (perimeter_n4*0.414+perimeter_n8*0.586)/1.055
    					 (unit: px)
    orientation         	:	 display 3 orientations (>0, =0, <0)
    angle               	:	 angle between the inertia axis and the normal
    					 abscissa axis
    circularity         	:	 4*pi*area/perimeter_n4_n8²
    thinness            	:	 perimeter_n4_n8/area
    isotropy            	:	 feret_diameter_min/feret_diameter_max
    mean_radius         	:	 mean radius
    stand_dev_radius    	:	 standard deviation of radius
    radius_variation    	:	 sum((r(i)-r(i+1))²)/n 
    					 i is a radius of the component, i+1 its adjacent radius
    					 n is the total number of radius of each component
    color_h_mean        	:	 mean value of hue
    color_s_mean        	:	 mean value of saturation
    color_v_mean        	:	 mean value of value (lightness)
    color_h_stand_dev   	:	 standard deviation of hue
    color_s_stand_dev   	:	 standard deviation of saturation
    color_v_stand_dev   	:	 standard deviation of value (lightness)
    color_r_mean        	:	 mean value of red
    color_g_mean        	:	 mean value of blue
    color_b_mean        	:	 mean value of green
    color_r_stand_dev   	:	 standard deviation of red
    color_g_stand_dev   	:	 standard deviation of blue
    color_b_stand_dev   	:	 standard deviation of green
    [default value: boundingbox]
    
    Attention : when input labelled image is 8-connected, 
    edge_n4 and edge_n4_order are not suggested.

[ -sec <boolean> ]
    Visualize a section of a grand image
    If true, visualize only one component among all components.
    boundingbox and boundingbox_voronoi do not work here.
    To use it, combined with option -l.
    [default value: false] 

[ -l <vector of S32> ]
    choice of label (from 1 to the maximum number of components)
    Choose some labels to visualize a feature about only these components.
    Use only when -sec is true
    [default value: maximum label of components] 

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsCorrectImages


    AimsCorrectImages
    -----------------

Correct pixels intensity in the overlapping region of a pair of images (Mosaic
reconstruction)

Options :

-ref <string>
    Input reference image (Top or Left)

-test <string>
    Input test image (Bottom or Right)

-tx <S32>
    translation along X axis

-ty <S32>
    translation along Y axis

-d <S32>
    mosaicing direction axis
    1 : Horizontal
    2 : Vertical

-type <S32>
    Data type : 
    S16 : 1 
    U8 : 2 
    FLOAT : 3 
    RGB : 4 

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsCreateFieldsFromMotion


    AimsCreateFieldsFromMotion
    --------------------------

Create the resampling field from a motion

Options :

-m <string>
    Input motion

-r <string>
    Reference image

-o <string>
    Output field

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsEntropicThresholding


    AimsEntropicThresholding
    ------------------------

Entropic thresholding

Options :

-i <file name (read only): volume of U8>
    Input grey-level image

[ -b <S32> ]
    Binary threshold or not [default : 0]

[ -min <U8> ]
    Minimal value of the entropic threshold [default : 1] 

[ -max <U8> ]
    Minimal value of the entropic threshold [default : 255]

-o <filename: volume of U8>
    Output image

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsEqualizer


-------------------------------------------------------------------------
AimsEqualizer    -i [eference] <ref>                                     
                 -o [utput] <fileout>                                    
                                                                         
                                                                         
               [-h[elp]]                                                 
-------------------------------------------------------------------------

AimsFovCentering


    AimsFovCentering
    ----------------

Generate .trm file to center FOV

Options :

-i <string>
    Input image 1

-j <string>
    Input image 2

[ --inv <boolean> ]
    Generate inverted motion

[ -o <string> ]
    Output motion

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsGenerateVolume


    AimsGenerateVolume
    ------------------

Creates empty volumes on disk. It may be used for later partial writing.
Currently GIS is the only supported format.

Options :

-o <string>
    Output file name

[ -t <string> ]
    Output data type (default: S16)

[ -sx <S32> ]
    Output size in X (default: 1)

[ -sy <S32> ]
    Output size in Y (default: 1)

[ -sz <S32> ]
    Output size in Z (default: 1)

[ -st <S32> ]
    Output size in T (default: 1)

[ -vx <DOUBLE> ]
    Output voxel size in X (default: 1.0)

[ -vy <DOUBLE> ]
    Output voxel size in Y (default: 1.0)

[ -vz <DOUBLE> ]
    Output voxel size in Z (default: 1.0)

[ -vt <DOUBLE> ]
    Output voxel size in T (default: 1.0)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel | -d <S32> ]
    Set debug information level (default = 0)

[ --verbose | -v [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsGridCalibrate


    AimsGridCalibrate
    -----------------

Processes voxel sizes using a grid image.
Voxel sizes can be set on input image directly.

Options :

-i <file name (read only): { Volume of RGB, Volume of RGBA, Volume of S16,
    Volume of S32, Volume of S8, Volume of U16, Volume of U32, Volume of U8 }>
    Input image containing a regular grid.

[ -o <string> ]
    Output file to set with estimated voxel size.

[ -b <string> ]
    Output BuckeMap file contaning mass centers used to process voxel size.

[ -c <S32> ]
    Channel of multi-channel image to use during voxel size estimation
    Possible types and values:
    type : RGB or RGBA
    values: 0=red, 1=green, 2=blue, 3=alpha, 4=norm
    
    type : HSV
    values: 0=hue, 1=saturation, 2=value, 4=norm
    
    [default is set to norm]
    

[ -d <DOUBLE> ]
    Distance (in mm) between grid points [default: 1]

[ -m <string> ]
    mode that can be:
    lt   --> lower than
    le   --> lower or equal to
    gt   --> greater than
    ge   --> greater or equal to
    eq   --> equal to
    di   --> differ
    [default: ge]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose | -v [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsGridGenerate


    AimsGridGenerate
    ----------------

Generate 3D regular grid image

Options :

-o <string>
    output image

[ --rx <S16> ]
    X sampling, each plane is generated every X voxels (default: 2)

[ --ry <S16> ]
    Y sampling, each plane is generated every Y voxels (default: 2)

[ --rz <S16> ]
    Z sampling, each plane is generated every Z voxels (default: 2)

[ --ox <S16> ]
    X offset to start grid generation (default: 0)

[ --oy <S16> ]
    Y offset to start grid generation (default: 0)

[ --oz <S16> ]
    Z offset to start grid generation (default: 0)

[ --dx <S16> ]
    dimx of grid image

[ --dy <S16> ]
    dimy of grid image

[ --dz <S16> ]
    dimz of grid image

[ --sx <FLOAT> ]
    voxel x dimension of the grid volume

[ --sy <FLOAT> ]
    voxel y dimension of the grid volume

[ --sz <FLOAT> ]
    voxel z dimension of the grid volume

[ -r <string> ]
    Volume used to define output voxel size and volume dimension (values are
    overrided by --dx, --dy, --dz, --sx, --sy and --sz)

[ -t <string> ]
    output data type (default: same as reference or S16 if no reference is
    specified)

[ --gt <S32> ]
    grid type (1: grid of planes, 2: grid of lines, 3: grid of dots, 4:
    chessboard, default: 1)

[ --fg <string> ]
    foreground voxel intensity (default: 255)

[ --bg <string> ]
    background voxel intensity (default: 0)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsHeightFiltering


    AimsHeightFiltering
    -------------------

Height filtering

Options :

-i <file name (read only): volume of U8>
    Input grey-level image

-height <U8>
    Height of the filter

[ -b <S32> ]
    Binary threshold or not [default : 0]

[ -c <U8> ]
    Connexity 4 or 8 [default : 4]

-o <filename: volume of U8>
    Output image

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsIndexCluster


    AimsIndexCluster
    ----------------

Automatically index SPMclusters using an atlas segmentation
--> compute Vol_cluster (mm3) / ROI

only for volumes of labels (same dim + voxel_size)
ROIs must have same label in both volumes

Options :

[ -r <file name (read only): { Volume of DOUBLE, Volume of FLOAT, Volume of S16,
    Volume of S32, Volume of S8, Volume of U16, Volume of U32, Volume of U8 }>
    Input atlas data ]

[ -t <string> ]
    Input cluster data

[ -o <string> ]
    Output textfile

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsIndividSlices


    AimsIndividSlices
    -----------------

Individualize and stack slices from multiple scan

Options :

-i <string>
    Input original image

[ -pi <string> ]
    Input preprocessed image

[ -f <string> ]
    force a specific output format (GIS, TIFF, ...) (default: GIS)

[ -c <U8> ]
    Channel to use to process multi-channel image
    Possible types and values:
    type : RGB or RGBA
    values: 0=red, 1=green, 2=blue, 3=norm
    
    type : HSV
    values: 0=hue, 1=saturation, 2=value, 3=norm
    

-n <S32>
    Number of slices

[ --dimsizes <vector of S32> ]
    Dimensions sizes

[ --dimorders <vector of S32> ]
    Dimensions orders

[ -nostack <boolean> ]
    Specify that individualized slices must not be stacked.
    In that case, individualized slices are stored in the output directory.

-z <FLOAT>
    Inter slice space (in mm)

-res <S32>
    Scan resolution (in dpi)

[ -dx <S32> ]
    X dimension of the final volume

[ -dy <S32> ]
    Y dimension of the final volume

[ -lt <S32> ]
    Lower threshold [manual activation]

[ -ht <S32> ]
    Higher threshold [manual activation]

-ms <S32>
    Minimal surface of slices [in mm2]

[ -sn <U8> ]
    First slice number (use only with -nostack option)

[ -nm <string> ]
    Output image name (use only with -nostack option)

[ -tf <FLOAT> ]
    Test fraction to use for dimension and surface variations

[ -o <string> ]
    Output stacked image or directory (depending on -nostack option)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsInterlaceVolumes


    AimsInterlaceVolumes
    --------------------

Interlacing multiple volumes in resulting one

Options :

[ -i <vector of string> ]
    Input volumes to interlace

[ -o <string> ]
    Output interlaced volume

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsLabelReorder


    AimsLabelReorder
    ----------------

Reorder labels of connected components volume (data type : S16)

Options :

-i <string>
    Input volume label

[ --dimsizes <vector of S32> ]
    Dimensions sizes [dimX dimY dimZ]

[ --dimorders <vector of S32> ]
    Dimensions orders [X_Order, Y_Order, Z_Order]([0 1 2], [1 0 2], etc.)
    (default = [0 1 2])

-o <string>
    Output labeled volume in the selected order

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMIBucketRegister


-------------------------------------------------------------------------
AimsMIBucketRegister  -r[eference] <ref (bucket_SHORT file)>                   
                -t[est] <test >                                          
                -o[utput] <fileout>                                      
               [--serialnum  <sn>]                                       
               [--Tx   <Tx>]                                             
               [--Ty   <Ty>]                                             
               [--Tz   <Tz>]                                             
               [--dTx <dTx>]                                             
               [--dTy <dTy>]                                             
               [--dTz <dTz>]                                             
               [--Rx <Rx>]                                               
               [--Ry <Ry>]                                               
               [--Rz <Rz>]                                               
               [--dRx <dRx>]                                             
               [--dRy <dRy>]                                             
               [--dRz <dRz>]                                             
               [--interpolation <method>]                                
               [--optimization <algo>]                                   
               [--pdfcalc <mode>]                                        
               [--gcinit <mode>]                                         
               [--index <index>]                                         
               [--pays_size <pays_size>]                                 
               [--graylevel <nl>]                                        
               [--masksize <ms>]                                         
               [--error <epsilon>]                                       
               [-h[elp]]                                                 
-------------------------------------------------------------------------
Registration according to Mutual Information Method                       
-------------------------------------------------------------------------
     ref        : source S16 reference data                              
     test       : source S16 test data (to register)                     
     fileout    : destination S16 data                                   
     sn         : number of the frame to consider for ref [default 0]    
                :      relevant for dynamic series ref images            
     Tx, Ty, Tz : Init Translaction coord   [default=0.0,0.0]            
     Rx, Ry, Rz : Init Rotation coord       [default=0.0,0.0]            
     dWw        : Increment for variable Ww [default=heuristics in code] 
     method     : interpolation  nearest/linear/spline [default=linear]  
     algo       : optimaizer  powell/random/single [default=powell]      
                       single --> get a one shot evaluation              
                       random --> sample cost value in a given area      
                       powell --> cost minimization with powell algorithm
     index      : index to be optimized mi/cr     [default=mi]           
                       Mutual Information --> mi                         
                       Correlation Ratio  --> cr                         
     mode       : Pdf calculus mode : direct(def) ou pv                  
     pays_size  : Half size the volume generated if algo=other activated 
     nl         : numb of classes in histogram pdf estimation [def.=64]  
     ms         : size of the gaussian convolution mask in pdf estimation
                         for Mutual Information         [default=5]      
     seuilref   : relative thresh applied prior to grav cent estimation  
     seuiltest  :                                                        
                                                                         
     epsilon    : tolerance on results [default=0.00001]                 
     gcinit     : Init with GravCenter : "yes" (def.) or "no"        
-------------------------------------------------------------------------

AimsMaskContour


    AimsMaskContour
    ---------------

Contour image visualization

Options :

-i <string>
    Input mask image

[ -ic <boolean> ]
    Generate input contour [default=true]

[ -oc <boolean> ]
    Generate output contour [default=true]

-o <string>
    Output contour image

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMergeFFDLabels


    AimsMergeFFDLabels
    ------------------

Merge FFD labels

Options :

--atlas <string>
    Input Atlas

--coef <string>
    Input Coefficient Image

--curcoef <file name (read only): volume of S16>
    Input Current Coefficient Image

[ -l <S16> ]
    Current label processed

[ -t <FLOAT> ]
    Threshold [Default : 0.5 * value]

[ -v <S16> ]
    Value for FFD processing [Default : 16000]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshMatching


    AimsMeshMatching
    ----------------

Registration of a mesh on a binary image, by affine deformation

Options :

-r | --reference <file name (read only): volume of S16>
    Reference binary image

-t | --test <file name (read only): Mesh of VOID>
    Test mesh

[ --transfo <string> ]
    Specify transformation: RIGID/SIMILARITY/AFFINE [default=AFFINE]

[ --trm <filename: AffineTransformation3d> ]
    File to save optimal transformation [default=[transfo]_[ref]_TO_[test].trm]

[ --trmInv <filename: AffineTransformation3d> ]
    File to save inverse transformation [default=[test]_TO_[ref].trm]

[ --mesh <filename: Mesh of VOID> ]
    File to save the resulting mesh [default=no saving file]

[ --gcinit <string> ]
    Initialize translation with gravity centers: yes/no [default=yes]

[ --log <string> ]
    Log reporting the running process [default=no log]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMidPlaneMask


    AimsMidPlaneMask
    ----------------

Compute left/right mask from mid-plane equation.
1 is right
2 is left
At least one of "input" and "mask" must be filled.

Options :

[ -i | --input <file name (read only): { Volume of DOUBLE, Volume of FLOAT,
    Volume of RGB, Volume of RGBA, Volume of S16, Volume of S32, Volume of S8,
    Volume of U16, Volume of U32, Volume of U8 }>  Input image. ]

-p | --plane <string>
    Input mid-plane equation.

[ -m | --mask <string> ]
    Input mask.

-o | --output <string>
    Output side mask.

[ --radio <boolean> ]
    Radiological orientation [default: false]

[ --type <string> ]
    Output data type [default: S16]

[ --bv <string> ]
    Background value in mask [default: 0]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel | -d <S32> ]
    Set debug information level (default = 0)

[ --verbose | -v [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMosaic


    AimsMosaic
    ----------

Reconstruct an image mosaic from a list of images.

Options :

-i <string>
    Input list of images (add a ' *' at the end of a line in the list if the
    corresponding image is empty)

-x <S32>
    Number of images along X

-y <S32>
    Number of images along Y

-t <S32>
    Data type : 
    S16 : 1 
    U8 : 2 
    FLOAT : 3 
    RGB : 4 

-o <string>
    Output reconstructed image

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMultiRecal


    AimsMultiRecal
    --------------

Compute registrations between two 2D or 3D volumes

Options :

-r <string>
    input reference data

-t <string>
    input test data

[ --roi <string> ]
    input roi test data (default : connex components research)

[ -o <string> ]
    output data

[ -m <string> ]
    initialisation motion (default = identity)

[ --start <S32> ]
    starting pyramid level (default = auto)

[ --stop <S32> ]
    end pyramid level (default = auto)

[ --transfo <S32> ]
    transformation type : 1 for rigid, 2 for similitude, 3 for affine (default
    = 1)

[ --Xsize <S16> ]
    x size of the bloc in voxel (default = 4)

[ --Ysize <S16> ]
    y size of the bloc in voxel (default = 4)

[ --Zsize <S16> ]
    z size of the bloc in voxel (default = 4)

[ --cutVar <DOUBLE> ]
    initial % of the blocks with highest variance kept (default=auto)

[ --stopVar <DOUBLE> ]
    minimum of this % of blocks kept (default=auto)

[ --%kept <DOUBLE> ]
    % of blocks of lowest residuals kepts for the robust estimation
    (default=0.5)

[ --radius <FLOAT> ]
    radius of the maximum erosion in voxels (default = 5)

[ --correlThresh <DOUBLE> ]
    threshold on the similarity criterion norm (default=-1, no threshold)

[ --lthRef <S16> ]
    low grey level threshhold on ref image (default = -100000)

[ --hthRef <S16> ]
    high grey level threshhold on ref image (default = +100000)

[ --lthTest <S16> ]
    low grey level threshhold on test image (default = -100000)

[ --hthTest <S16> ]
    high grey level threshhold on test image (default = +100000)

[ --iter <S32> ]
    maximum number of iterations per pyramid level (default=3)

[ --field <string> ]
    Displacement field (sorry, not active)

[ --Info <string> ]
    list all the initial parameters : y or n (default=y)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsOverlapInfo


    AimsOverlapInfo
    ---------------

Processes DICE comparison between label image(s) and ROI graph(s).

Options :

-i <list of string>
    Input label image(s) used as test image in DICE comparison

-g <list of string>
    ROI Graph(s). ROI are used as reference in DICE comparison

-l <vector of U32>
    Labels of input image(s) to use in DICE comparison

-r <vector of string>
    ROI of graph(s) to use in DICE comparison

[ -o <filename: volume of DOUBLE> ]
    Output DICE image

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose | -v [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsPointsExtreme


    AimsPointsExtreme
    -----------------

Components features computing

According to 2 basic images (color image, grayscale image), 
calculate extreme points in a circle with a predefined radius.
An extreme point in a larger circle is more confident.

Options :

-col <string>
    Input color image to read

-i <string>
    Input image to read

[ -o <string> ]
    Output image

[ -min <string> ]
    Output image minimum

[ -r <S32> ]
    work on method maximum, find maximal points in a certain range
    [default: '1']

[ -aim <string> ]
    the principal local extreme points
    
    maximum 	:	 to find strict maximum
    minimum 	:	 to find strict minimum
    [default: 'minimum']

[ -w <string> ]
    weights of each iteration
    equal
    nonequal
    [default: 'equal']

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsRebuildComp


    AimsRebuildComp
    ---------------

Rebuild connected components using seeds.

Options :

-s <file name (read only): volume of S16>
    Input image seed / connected component

-m <file name (read only): volume of S16>
    Input image mask / segmentation

-o <filename: volume of S16>
    Output image of separated components

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsResampleFromFieldsData


    AimsResampleFromFieldsData
    --------------------------

Resample an image from a resampling field

Options :

-i <string>
    Input image

-f <string>
    Resampling field data

-t <S32>
    Data type : 
    S16 : 1 
    U8 : 2 
    FLOAT : 3 
    RGB : 4 

-o <string>
    Output resampled image

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsRgbToHsv


    AimsRgbToHsv
    ------------

RGB-HSV conversion

Options :

-i <string>
    Input RGB image

[ -ov <string> ]
    Output value image

[ -os <string> ]
    Output saturation image

[ -oh <string> ]
    Output hue image

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsRoiOverlap


    AimsRoiOverlap
    --------------

Compute overlapping criteria to compare quantitatively two segmentations

only for volumes of labels (same dim + voxel_size)
ROIs must have same label in both volumes

#############################################################################
		   2 * | VolTest_lab(i) - VolRef_lab(i) | 
Vol_Diff_lab(i) = ----------------------------------------
		       VolTest_lab(i) + VolRef_lab(i)

		2 * intersection ( VolTest_lab(i),VolRef_lab(i) ) 
Dice_lab(i) = -----------------------------------------------------
			VolTest_lab(i) + VolRef_lab(i)

		    intersection ( VolTest_lab(i),VolRef_lab(i) ) 
Jaccard_lab(i) = ---------------------------------------------------- 
			union ( VolTest_lab(i),VolRef_lab(i) )

			intersection ( VolTest_lab(i),VolRef_lab(i) )
Sensitivity_lab(i) = --------------------------------------------------- 
					VolRef_lab(i)

#############################################################################

Options :

[ -r <file name (read only): { Volume of DOUBLE, Volume of FLOAT, Volume of S16,
    Volume of S32, Volume of S8, Volume of U16, Volume of U32, Volume of U8 }>
    Input reference data ]

[ -t <string> ]
    Input test data

[ -o <string> ]
    Output textfile

[ -matrix <string> ]
    Output image

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSamplingInfo


    AimsSamplingInfo
    ----------------

Estimate optimal sampling to perform morphometric analyses

Options :

-i <file name (read only): volume of S16>
    Input labeled atlas data

[ -f <S16> ]
    Maximal interval [Default: 1/1 section]

[ -s <FLOAT> ]
    Voxel size [Default: atlas voxelsize]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSeededWatershed


    AimsSeededWatershed
    -------------------

Seeded watershed.
A front propagation is computed from the seeds, with 

Options :

[ -i | --input <file name (read only): { Bucket of S16, Bucket of S32, Bucket
    of U16, Bucket of U32, Bucket of VOID, Volume of S16, Volume of S32, Volume
    of S8, Volume of U16, Volume of U32, Volume of U8 }>  Input gray level
    volume.
    ]

-s | --input-seeds <file name (read only): { Volume of DOUBLE, Volume of FLOAT,
    Volume of S16, Volume of S32, Volume of S8, Volume of U16, Volume of U32,
    Volume of U8 }>  Input seeds.

-o | --output <string>
    Output watershed volume.

[ -d | --output-distance <string> ]
    Output distance volume.

[ -l | --seed-labels <vector of S16> ]
    Seed labels [default: 1]

[ -w | --work-labels <vector of S16> ]
    Work labels [default: 0]

[ --inv | --invert-speedmap <boolean> ]
    Invert speedmap [default: false].
    The default parameter works with seeds close to minima of the gray level
    image (objects of interest are dark). If seeds are close to maxima (object
    of interest are bright), inv needs to be true.

[ -t | --type <string> ]
    Output data type (S16 [default], S32, ...)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose | -v [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSegment2Modes


    AimsSegment2Modes
    -----------------

Segmentation based on adaptive thresholding

Options :

-r <file name (read only): volume of S16>
    Input image RED

-g <file name (read only): volume of S16>
    Input image GREEN

-s <S64>
    minimum size

[ --clo <boolean> ]
    morpho math [Default=no]

[ -e <FLOAT> ]
    radius

-m <filename: volume of S16>
    Mask image

[ --correct <boolean> ]
    Apply a correction to green component [Default=no]

-o <filename: volume of S16>
    Output image GREEN

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSeparateComp


    AimsSeparateComp
    ----------------

Separate connected components using erosion until
the number of expected components is reached.

Options :

-i <file name (read only): volume of S16>
    Input image of segmented component

[ -r <FLOAT> ]
    Ratio concerning mean size [Default=100%]

-n <S32>
    Number of connected components expected

-o <filename: volume of S16>
    Output image of connected components

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsStereologySampling


    AimsStereologySampling
    ----------------------

Stereology sampling estimation

Options :

-i <file name (read only): volume of S16>
    Binary image (segmented)

-m <file name (read only): volume of S16>
    Mask image (tissue)

[ -max <S32> ]
    Max sampling value [default : 50]

[ -r <string> ]
    Results file (txt format)

-o <filename: volume of S16>
    Grid file

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsStereotaxy


    AimsStereotaxy
    --------------

Reads a graph, compute stereotaxic distances

Options :

-t <string>
    Text file *.txt

-g <string>
    Input graph name

[ -n <S32> ]
    Plane number [Default: n=1]

-m <string>
    Output mesh name [Extension *.mesh

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsWatershed


    AimsWatershed
    -------------

Compute watershed segmentation.

Options :

-i <file name (read only): { Volume of DOUBLE, Volume of FLOAT, Volume of S16,
    Volume of S32, Volume of S8, Volume of U16, Volume of U32, Volume of U8 }>
    Input grayscale image.

-o <string>
    Output segmented image.

[ -t <string> ]
    Output data type (S16 [default], S32, ...)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel | -d <S32> ]
    Set debug information level (default = 0)

[ --verbose | -v [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


bioClusterStatistics


    bioClusterStatistics
    --------------------

Detection of clusters in statistics volumes. 
Clusters can be filtered by size, mass (T statistic sum over the cluster) and
height(T statistic/Cluster Size)

Options :

-it <string>
    Input T statistic image

-ip <string>
    Input p-values image

-im <string>
    Input mask image

[ -a <DOUBLE> ]
    Alpha risk. Default: 0.05

[ -p <S32> ]
    P-values correction for multiple comparisons. 
    Can be either: 0 (None), 1 (Bonferroni), 2 (False Discovery rate). Default:
    None.

[ --msize <S32> ]
    Minimum cluster size (voxels). Default: 0

[ --mmass <DOUBLE> ]
    Minimum cluster mass. Default: 0

[ --mheight <DOUBLE> ]
    Minimum cluster height. Default: 0

[ -c <string> ]
    Cluster 3D connectivity. It can only take the following values:6, 18
    (default), 26.

[ -oc1 <string> ]
    Output clusters (group1 > group2)

[ -oc2 <string> ]
    Output clusters (group2 > group1)

[ -ot <string> ]
    Compute clusters size (voxels), mass (sum of the T statistics) and height
    (mean of the T statistics)and stores it into a text file.

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


bioExtractAmyloidLoad


    bioExtractAmyloidLoad
    ---------------------

Extract amyloid load from output AimsAmyloidFiltering text file

Options :

-i <string>
    input file BioVision

[ -r <string> ]
    input file Image J

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


bioExtractDice


    bioExtractDice
    --------------

Extract Dice indices from output txt file of my script to test clustering
parameters and creates a Volume of Dice

Options :

-i <string>
    input Dice file

-o <filename: volume of FLOAT>
    Output C image

[ -v <boolean> ]
    verbose

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


bioFindCellSeeds


    bioFindCellSeeds
    ----------------

Compute cell seeds from histology image.

Options :

-i <file name (read only): { Volume of DOUBLE, Volume of FLOAT, Volume of RGB,
    Volume of RGBA, Volume of S16, Volume of S32, Volume of S8, Volume of U16,
    Volume of U32, Volume of U8 }>  Input image.

[ -m <string> ]
    Input cell mask image

[ -o <string> ]
    Output seed image.

[ -b <string> ]
    Output seed bucket.

[ -c <string> ]
    Channel to use if color image: n[orm] (default), r[ed], g[reen], b[lue],
    h[ue], s[aturation], v[alue], y [luminance], cb [blue chrominance], cr [red
    chrominance]

[ --wall <boolean> ]
    write all levels (debug option)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel | -d <S32> ]
    Set debug information level (default = 0)

[ --verbose | -v [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


bioMacGetSingleBrain


    bioMacGetSingleBrain
    --------------------

Get 2D macaque brain mask from 2D photo.
BioVision classes must be named 'artifact','brain','coat'. If it is not the
case, use -c options to specify classes names.

Options :

-i <file name (read only): { Volume of RGB, Volume of RGBA }>  Input image.

-l <string>
    Input learning set (biovision).

-o <string>
    Output brain mask image.

[ -c <vector of string> ]
    Classes names a/b/c (default:artifact brain coat)

[ -p <vector of DOUBLE> ]
    Prior for classes a/b/c (default:1/3)

[ -b <boolean> ]
    Extract biggest composent at the end (default:false)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel | -d <S32> ]
    Set debug information level (default = 0)

[ --verbose | -v [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


bioVoxelFeatures


    bioVoxelFeatures
    ----------------

Extract features from an image.

Features can be either stored in the T dimension in which case, the voxels keep
their X, Y, Z position or according to the Y dimension, in which case voxels
are sorted along the X axis.

Color features are RGB or HSV or Gray. 

Local color features include mean and variance in a given neighborhood defined
by the structural element

Texture features include Gabor filters reponses. Gabor filters require that
several parameters are specified. Based on the given parameters, a family of
filters will be created with all possible combinations of parameters.The image
is then filtered which each member of the family.

Options :

-i <string>
    Input image

-o <string>
    Output image

[ -of <string> ]
    Output features dictionary

[ -r <boolean> ]
    Output reshaped feature vector. Default: False.

[ -c <string> ]
    Extract color channels: RGB, HSV or None. Default = None.

[ -nmean <boolean> ]
    Extract mean neighborhood intensity in the gray value image. Default =
    False.

[ -nvar <boolean> ]
    Extract variance from neighborhood intensity in the gray value image.
    Default = False.

[ -nwind <boolean> ]
    Use a circular window around each voxel as features. Default = False.

[ -na <S32> ]
    Amplitude of the neighboring structuring element (voxels). Default = 1.

[ -layers <vector of S32> ]
    Extract concentring layers around each pixel and store each element of the
    layers as a feature.Radius for each layer should be specified in voxels.

[ -g <boolean> ]
    Gabor filtering on the gray converted image. Default = False.

[ -sigma <vector of DOUBLE> ]
    Gabor sigma parameter list (voxels).

[ -theta <vector of DOUBLE> ]
    Gabor theta parameter list (degrees).

[ -lambda <vector of DOUBLE> ]
    Gabor lambda parameter list (voxels).

[ -psi <vector of DOUBLE> ]
    Gabor psi parameter list.

[ -gamma <vector of DOUBLE> ]
    Gabor gamma parameter list.

[ -real <vector of S32> ]
    Gabor real parameter list (0: imaginary or 1: real).

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


bioVoxelWiseStatistics


    bioVoxelWiseStatistics
    ----------------------

Performs a voxel-wise t-test. All images should have same voxel-sizes !

Options :

-m <string>
    Input mask wherein voxel-wise t-test will be performed (S16).

-g1 <vector of string>
    List of input images for group 1.

-g2 <vector of string>
    List of input images for group 2.

[ -t <S32> ]
    t-test tail. 1: one-tailed, 2: two-tailed. Default: 2.)

[ -ot <string> ]
    Output T statistic image

[ -op <string> ]
    Output p-values image

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsRegisterQNEstimate


    AimsRegisterQNEstimate
    ----------------------

Affine registration by index minimization.

Options :

--test | -i | -t <string>
    Test image (to be registered).

--reference | -r <string>
    Reference image

--output | -o <string>
    Output motion.

[ --motion-init | -m <string> ]
    Input init motion.

[ --channel-reference | -cr <string> ]
    Channel to use if color image: r[ed], g[reen], b[lue], n[orm] (default)

[ --channel-test | -ct <string> ]
    Channel to use if color image: r[ed], g[reen], b[lue], n[orm] (default)

[ --points <string> ]
    Estimation points (in the reference image referential. (default: use all
    voxels. see also --stride)

[ --transformation | -tr <string> ]
    Transformation type: t[ranslation], r[igid], s[imilitude], a[ffine]
    (default: tra)

[ --optimizer | -op <string> ]
    Optimizer: p[owell], b[fgs], l[bfgs], n[ewton], t[rust-newton] (default :t)

[ --function | -f <string> ]
    Function to minimize: c[r] {correlation ratio}, m[i] {mutual information}
    (default: mi)

[ --regularize | -reg <string> ]
    Regularization term: 0 {none} (default), 1 {l1 norm}, 2 {l2 norm}

[ --pyramid <string> ]
    Pyramid mode: l[east square] {more precise} (default), m[oving average]
    {faster}

[ --stop <FLOAT> ]
    Stop criterion (default: 1E-5)

[ --trust <FLOAT> ]
    Trust radius (for newton mode) (default: 1.)

[ --stride <S32> ]
    Stride used to select reference points (only if --points is not used).
    (default: 1)

[ --exact-hessian | -eh <boolean> ]
    Do not approximate the Hessian matrix with Newton optimizer (default:
    false)

[ --level-start | -lb <S32> ]
    Pyramid level at which to start the registration (default: auto)

[ --level-stop | -le <S32> ]
    Pyramid level at which to end the registration (default: auto)

[ --level-incr | -li <S32> ]
    Increment between pyramid levels (default: auto)

[ --gc-init <string> ]
    Gravity center initialization w[eighted] (default), u[nweighted], n[one]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel | -d <S32> ]
    Set debug information level (default = 0)

[ --verbose | -v [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSegmentationEM


    AimsSegmentationEM
    ------------------

Segmentation by Expectation-Maximization.


Options :

-i | --input <file name (read only): { Volume of DOUBLE, Volume of FLOAT,
    Volume of RGB, Volume of RGBA, Volume of S16, Volume of S32, Volume of S8,
    Volume of U16, Volume of U32, Volume of U8 }>  Input image.

[ -c | --channel <S32> ]
    Channel to use if color image: 0 [red], 1 [green], 2 [blue], 3 [alpha], 4
    [norm] (default)

[ -p | --input-prior-map <string> ]
    Class probability image (classes are in the T dimension)

[ -cm | --input-clique-matrix <string> ]
    MRF clique matrix (default: diag(1))

[ -m | --input-mask <string> ]
    Mask in which to compute the classification

[ -bf | --input-bias-field <string> ]
    Input multiplicative bias field

[ -o | --output <string> ]
    Output segmentation.

[ -op | --output-probabilities <string> ]
    Output probabilites

[ -onb | --output-no-bias <string> ]
    Output bias corrected image

[ -obf | --output-bias-field <string> ]
    Output multiplicative bias field

[ -n | --n-classes <S32> ]
    Number of classes (only necessary in the most basic case with no parameter
    provided)

[ --mu <vector of FLOAT> ]
    Initial mean values for the normal distributions.

[ --sigma <vector of FLOAT> ]
    Initial standard deviation values for the normal distributions.

[ --alpha <vector of FLOAT> ]
    Initial values for the stationary prior. They only make sense if no prior
    map is provided. If prior type is non-stationary, priors will be
    initialized with these values but their updated values won't stay
    stationary.

[ --stop-crit <string> ]
    Stop criterion for Log-Likelihood Sum:
    - g[ain] (default)
    - a[bs diff]

[ --stop-value <FLOAT> ]
    Stop criterion value (default: 0.01)

[ --iter-min <S32> ]
    Minimum number of iterations (default: 2)

[ --iter-max <S32> ]
    Maximum number of iterations (default: 100/nclasses)

[ --init-normal <string> ]
    Initialization mode for the normal distribution. It only makes sense if no
    mu/sigma and no prior map was provided.
    - r[andom] (default)
    - f[rom prior]
    - k[means]
    - kmeans++
    - p[rovided]

[ --prior-type <string> ]
    Force prior type:
    - s[tationary] (default if no prior map provided)
    - n[on-stationary]
    - m[ixed] (default if a prior map is provided)

[ --parameterize-prior <boolean> ]
    Make the prior a parameter in the EM algorithm. i.e. its values will be
    updated at each iteration with its maximum-likelihood estimation. If the
    prior is mixed, only the global class proportion, no the non-stationary
    prior, is updated. (default: true)

[ --smooth <FLOAT> ]
    Probability image smoothing sigma (no smoothing: 0, default: biggest voxel
    size)

[ --log <boolean> ]
    Log-transform intensities before EM (default: true)

[ --denoising <boolean> ]
    Enable denoising during EM (default: true)

[ --bias <string> ]
    Perform bias correction:
    - s[pline]
    - l[ow pass] (default)
    - n[one]

[ --bias-grid <vector of FLOAT> ]
    Bias grid (default: 10 10 10)

[ --bias-unit <string> ]
    Bias grid unit:
    - m[m]
    - v[oxel]
    - %[ of mri dimensions] (default)

[ --rf <string> ]
    Use of random fields for spatial regularization:
    - i[ter] (at each step of the EM algorithm) (default)
    - e[nd]  (at the end of a classical mixture model)
    - n[one] (no spatial regularization)

[ --rf-type <string> ]
    Class estimation method for the random field mode:
    - m[arkov] (clique potentials are kept as is and can be null) (default)
    - g[ibbs] (clique potential are exp transformed and are assured to be
    positive).

[ --rf-order <S32> ]
    Connectivity order for random field: 
    - 1 (2d: 4 / 3d: 6) (default)
    - 2 (2d: 8 / 3d: 18)
    - 3 (3d: 26)

[ --rf-eval <string> ]
    Class p method for the random field mode:
    - m[mp] (Maximum Marginal Probabilities) (default)
    - i[cm] (Iterated Conditional Mode).

[ --icm-iter-min <S32> ]
    Minimum number of ICM iterations (default: 1)

[ --icm-iter-max <S32> ]
    Maximum number of ICM iterations (default: 5)

[ --beta <FLOAT> ]
    Modulation of the neighborhood priors used in random fields. (default: 1)
    It consists in applying a beta power to the clique matrix before the
    eventual log transform (with gibbs fields). If beta == 0, all clique
    potentials are equal. If beta == 1, they are kept as is. In the gibbs case
    with the default diag(1) clique matrix, this is equivalent to Besag's beta
    parameter (in 'On the Statistical Analysis of Dirty Pictures', Julian Besag,
    1986)

[ --labels <vector of S32> ]
    List of labels corresponding to probability indices. (default: same). If
    several indices possess the same labels, their probabilities are merged.

[ --ignore <vector of S32> ]
    List of labels to exclude from the prior map.

[ --exclude <vector of S32> ]
    List of labels to ignore when estimating bias field.

[ -w | --write-inter-files <string> ]
    Debug directory (if set, write intermediate files) (default: false)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel | -d <S32> ]
    Set debug information level (default = 0)

[ --verbose | -v [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSelectGradPoints


    AimsSelectGradPoints
    --------------------

Select a given number of points from a volume with higher probability with
higher gradient norm.

Options :

--input | -i <string>
    Input volume.

--output | -o <string>
    Output bucket.

[ --channel | -c <string> ]
    Channel to use if color image: r[ed], g[reen], b[lue], n[orm] (default)

--npoints | -n <S64>
    Number of points to extract.

[ --balance | -b <FLOAT> ]
    Equilibriate probabilities. Number in [0,1].
    - If 0, the density is kept as is.
    - If 1, all points are equiprobables
    (default: 0)

[ --zero | -z <boolean> ]
    Include points with null gradient when balancing. (default: false)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel | -d <S32> ]
    Set debug information level (default = 0)

[ --verbose | -v [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


bioKMeans


    bioKMeans
    ---------

Compute a K-Means classification of an RGB or HSV image.

Options :

-i | --input <file name (read only): { Volume of RGB, Volume of RGBA, Volume of
    S16, Volume of S32, Volume of S8, Volume of U16, Volume of U32, Volume of
    U8 }>  Input image.

-o | --ouput <string>
    Output classification image.

[ -k <S32> ]
    Number of classes [default: 3].

[ -m <vector of DOUBLE> ]
    Initial means [default: random]

[ -e <vector of DOUBLE> ]
    Excluded values [default: none]

[ -r <S32> ]
    Maximum number of runs [default: 5]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSparseMatrixSmoothing


    AimsSparseMatrixSmoothing
    -------------------------

Sparse matrix smoothing using heat diffusion or gaussian 
smoothing, with the geometry of a mesh. Can typically be used for 
connectivity matrix smoothing. Smoothing is applied for each line, 
each line is a texture for the mesh.

Options :

-i <string>
    input sparse matrix

-m <file name (read only): Mesh of VOID>
    input mesh

-o <string>
    output sparse matrix

-s <DOUBLE>
    sigma equivalent of the smoothing

[ -t <DOUBLE> ]
    threshold smoothing coefficients under this value (default: 0.0001)

-l <file name (read only): texture of S32>
    label texture

-p <S32>
    patch index (num in label texture)

[ -g <boolean> ]
    use gaussian smoothing. Default is heat diffusion

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


constelBundlesFiltering


    constelBundlesFiltering
    -----------------------

Selection of tracking fibers according to a white matter mesh with 
label texture.

Options :

[ -i <vector of string> ]
    Bundle File input

-o <string>
    Bundle File output

-n <string>
    Bundle File output for "distant fibers"

--mesh <file name (read only): Mesh of VOID>
    input mesh

--tex <file name (read only): texture of S16>
    labels input texture

-g <string>
    gyrus name for distant fibers filtering

[ --trs <string> ]
    transformation from t2 to anat

[ --intadd <S32> ]
    int to add to Bundle Names

[ --mode <string> ]
    mode of new bundles names : = Name1_Name2 or NameFront, or NameEnd,
    or NameFront_NameEnd, or Name1_Name2orNotInMesh (default)

[ --names <vector of string> ]
    list of string containing bundle names to be selected

[ -r <boolean> ]
    names are regular expressions

[ -l <FLOAT> ]
    minimum length for a "near cortex" fiber (default: 0)

[ -L <FLOAT> ]
    maximum length for a "near cortex" fiber (default: no max)

[ --nimlmin <FLOAT> ]
    minimum length for a "not in mesh" fiber (default: same as cortex)

[ --nimlmax <FLOAT> ]
    maximum length for a "not in mesh" fiber (default: same as cortex)

[ --verbose <boolean> ]
    show as much information as possible

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


constelConnectionDensityTexture


    constelConnectionDensityTexture
    -------------------------------

computes and writes connection density texture(s).
Modes supported:
(1) oneSeedRegion_to_targets (2) seedVertex_to_targets

Options :

-mesh <file name (read only): Mesh of VOID>
    input mesh

-connmatrixfile <string>
    input conn matrix filename.

-seedregionstex <file name (read only): texture of S16>
    input region texture : study a region in particular.

[ -outconntex <string> ]
    output mean connectivity texture file name.

[ -seedlabel <S32> ]
    input seed region label.
    0 to calculate the mean connectivity for all the regions:
    mat.shape = (seedRegionsNb, targetRegionsNb)
    if seed region label != 0:
    mat.shape = (seedRegionLabel vertex nb, targetRegionsNb)

[ -verbose <boolean> ]
    for more information.

[ -normalize <boolean> ]
    normalize connectivity matrix

[ -type <string> ]
    Connectivity types supported: 
    (1) oneSeedRegion_to_targets (2) seedVertex_to_targets
    default = oneSeedRegion_to_targets

[ -targetregionstex <file name (read only): texture of S16> ]
    target regions texture for the calculation 
    of the global connectivity matrix

[ -outconntargets <string> ]
    output connectivity targets texture file name. 
    (shape (1, targetsNb))

[ -connmatrix <string> ]
    output connectivity Matrix file name

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


constelConnectivityMatrix


    constelConnectivityMatrix
    -------------------------

computes and writes connection density texture(s).
Modes supported: (1) mesh_to_mesh (2) oneSeedRegion_to_mesh

Options :

-bundles <string>
    input bundles

-mesh <file name (read only): Mesh of VOID>
    input mesh

[ -targets <vector of string> ]
    input target meshes

-outconntex <string>
    output mean connectivity texture file name

[ -outtargetstex <vector of string> ]
    output mean connectivity texture file name (to targets meshes)

-trs <string>
    transform from t2 to anat

[ -matrixcompute <string> ]
    type of computing the connectivity matrix supported: 
    (1) meshclosestpoint (2) meshintersectionpoint 
    (3) meshintersectionpointfast, default = meshclosestpoint

[ -dist <DOUBLE> ]
    dist for the neighborhood around each vertex for smoothing the 
    connectivity matrix, default = 5.0

[ -wthresh <DOUBLE> ]
    weight threshold for thresholding the connectivity matrix, 
    default = 1.0

[ -distmax <FLOAT> ]
    mesh closest point minimum distance, default = 5.

[ -seedregionstex <file name (read only): texture of S16> ]
    input region texture. default = all the mesh

[ -seedlabel <S32> ]
    input seed region label. 0 to calculate the mean connectivity for 
    all the regions : 
    connMatrix.shape=(seedRegionsNb, targetRegionsNb); 
    = (seedRegionLabel vertex nb, targetRegionsNb) 
    if seed region label != 0

[ -verbose <boolean> ]
    show as much information as possible

[ -normalize <boolean> ]
    normalize connectivity matrix

-type <string>
    connectivity type: seed_mean_connectivity_profile, 
    default = seed_connection_density

[ -connfmt <string> ]
    input conn matrix format, .ima or binar_sparse; 
    default = binar_sparse

[ -connmatrix <string> ]
    connectivity matrix filename of the seed region, 
    size = (seedRegionVertexNb,meshVertexNb)

[ -vertexindextype <string> ]
    format for seedRegionVertexIndexFile: 
    =texture(.tex) or =text(.txt) or =both(.tex and .txt), 
    default =  

[ -seedvertexindex <string> ]
    seedlabel region vertex indexes file name

[ -lmin <U32> ]
    length min for fibers

[ -lmax <U32> ]
    length max for fibers

[ -log <boolean> ]
    log option, if = True, applies the ln(1 + x) to the connectivity 
    matrix, default = False

[ -logfile <string> ]
    log filename, in case of logOption = 1, store log matrix in 
    another file. 
    By default, store log matrix in connMatrixFileName

[ -roimask <file name (read only): volume of S16> ]
    input region roi mask: ribbon around the mesh, in the case of 
    connMatrixComputingType = meshintersectionpointfast

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


constelFibersLengths


    constelFibersLengths
    --------------------

Output Fibers Lengths in a text file

Options :

-i <string>
    input bundles

-o <string>
    output fibers_length text filename

[ -verbose <boolean> ]
    show as much information as possible

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


constelMeanConnectivityProfileFromMatrix


    constelMeanConnectivityProfileFromMatrix
    ----------------------------------------

Compute the connectivity profile(s). 
Modes supported: (1) mesh_to_mesh (2) oneSeedRegion_to_mesh

Options :

[ -connfmt <string> ]
    Input connectivity matrix format. 
    Formats supported: (1) .ima, (2) binar_sparse or (3) ascii_sparse 
    default = binar_sparse

-connmatrixfile <string>
    Input connectivity matrix filename.

-outconntex <string>
    Output mean connectivity profile filename.

-seedregionstex <file name (read only): texture of S16>
    Input initial cortical parcellation (e.g. gyri segmentation).

[ -seedlabel <S32> ]
    Input seed region label.
    0 to calculate the mean connectivity for all the regions: 
    mat.shape = (maxLabel, targetRegionsNb) 
    -> if seedLabel != 0 : 
    mat.shape = (seedLabel vertexNb, targetRegionsNb)

[ -seedregionstex2 <file name (read only): texture of S16> ]
    Second cortical parcellation.
    If you want to study a region in particular, 
    the input connectivity matrix correspond to the first seed region

-seedlabel2 <vector of S32>
    second input seed region label + an -seedregiontex2 entry, 
    to obtain a connectivity profile of a sub region 
    = (of label seedlabel2 in secondCorticalParcellation) 
    of the input seedregion (of label seedlabel)

[ -verbose <boolean> ]
    For more information.

[ -normalize <boolean> ]
    Normalize connectivity matrix.

-type <string>
    Connectivity types supported: 
    (1) seed_mean_connectivity_profile (2) seed_connection_density
    default = seed_connection_density

[ -outconnmatrix <string> ]
    Output connectivity matrix filename of the seed region,
    size = (seedRegionVertexNb,meshVertexNb)
    default = don't save

[ -outseedvertex <string> ]
    Output seedlabel region vertex index filename (txt file)

[ -outseedvertextex <string> ]
    Output seedlabel region profile filename (texture file)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


constelSelectBundlesFromNames


    constelSelectBundlesFromNames
    -----------------------------

Select bundles from the input bundles file.The bundle names to be selected are
specified by a names list.

Options :

-i <string>
    bundles input

-o <string>
    bundles output

[ -names <vector of string> ]
    list of string containing bundle names to be selected

[ -verbose <boolean> ]
    show as much information as possible

[ -r <boolean> ]
    names are regular expressions

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


constelSelectFibersFromMesh


    constelSelectFibersFromMesh
    ---------------------------

Selection of tracking fibers according to a white matter mesh with 
label texture.

Options :

-i <string>
    Bundle File input

-o <string>
    Bundle File output

-namesfile <string>
    BundleNames File output

-mesh <file name (read only): Mesh of VOID>
    input mesh

-tex <file name (read only): texture of S16>
    labels input texture

[ -trs <string> ]
    transformation from t2 to anat

[ -intadd <S32> ]
    int to add to Bundle Names

[ -mode <string> ]
    mode of new bundles names : = Name1_Name2 (default) or NameFront, 
    or NameEnd, or NameFront_NameEnd, or Name1_Name2orNotInMesh

[ -verbose <boolean> ]
    show as much information as possible

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsCheck2DCoordinates


    AimsCheck2DCoordinates
    ----------------------

[UNCOMPLETE DEBUG FUNCTION] Check that a 2D surface-based coordinate system is
OK (unicity)

Options :

-m | --mesh <string>
    input mesh

-x | --xcoord <string>
    latitude texture

-y | --ycoord <string>
    longitude texture

-o | --out <string>
    output sign texture

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsConformalMapping


    AimsConformalMapping
    --------------------

Spherical conformal parameterization of a mesh

Options :

-i | --input <string>
    input mesh

[ -dt | --deltat <FLOAT> ]
    time step (recommended : 0.1, nothing above that for stability)

[ -de | --deltae <FLOAT> ]
    energy variation threshold for convergence (recommended : 0.001)

-o | --output <string>
    output mesh

-l | --lat <string>
    latitude texture

-L | --lon <string>
    longitude texture

[ -t | --tuette <string> ]
    Tuette map precomputed mesh

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsConstraintCleaner


    AimsConstraintCleaner
    ---------------------

Cortical Constraints Cleaning (for cortical surface coordinate system)

Options :

-m | --inMesh <string>
    input Mesh

-t | --inTexCingularPole <string>
    input Texture Cingular Pole

-p | --inTexPoles <string>
    Poles Textures

-x | --inTexMer <string>
    input Texture Meridian Constraints

-y | --inTexPar <string>
    input Texture Parallel Constraints

-f | --inCorrFile <string>
    input Constraint Correspondance File

-g | --inProjFile <string>
    input Projected constraint Correspondance File

-a | --outMer <string>
    outut Texture Cleaned Meridian Constraints

-b | --outPar <string>
    output Texture Cleaned Parallel Constraints

-i | --constraint_distance <FLOAT>
    constraint distance parameter

-j | --curvature <FLOAT>
    curvature parameter

-k | --elasticity <FLOAT>
    elasticity parameter

-c | --context <S32>
    context

-s | --side <string>
    side (left or right)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsCoordinateGridMesh


    AimsCoordinateGridMesh
    ----------------------

generate iso-parameter lines from a mesh and textures

Options :

-m | --mesh <string>
    input mesh

-x | --xcoord <string>
    latitude texture (or -x for sulci)

-y | --ycoord <string>
    longitude texture (or -y for sulci)

-c | --coord <string>
    coordinates (r=regular, c=constraints, s=sillon)

-o | --out <string>
    output mesh

[ -d | -diameter <FLOAT> ]
    tubes diameter (default=0.25)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsCoordinatesTextureToMesh


    AimsCoordinatesTextureToMesh
    ----------------------------

Creates a mesh from 3 coordinates textures (x,y and z)

Options :

-i | --inputMesh <string>
    input mesh

-x | --inputx <string>
    texture_x

-y | --inputy <string>
    texture_y

-z | --inputz <string>
    texture_z

-o <string>
    output mesh

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsCoordinatesToIndex


    AimsCoordinatesToIndex
    ----------------------

get the index of a point from its 2D surface coordinates

Options :

-i | --inputMesh <string>
    input mesh

-l | --lat <string>
    latitude texture

-L | --lon <string>
    longitude texture

-x <FLOAT>
    latitude

-y <FLOAT>
    longitude

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsCoordinatesToTexture


    AimsCoordinatesToTexture
    ------------------------

Create 3 textures of node coordinates

Options :

-i | --inputMesh <string>
    input mesh

-x | --outx <string>
    texture_x

-y | --outy <string>
    texture_y

-z | --outz <string>
    texture_z

-l | --local <S32>
    local coordinates transo (yes=1, default=0)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsCorticalReferential


    AimsCorticalReferential
    -----------------------

Diffusion of mesh-based coordinates with constraints

Options :

-i <string>
    input Surface Mesh

-p <string>
    input Texture Parallel Constraints

-m <string>
    input Texture Meridian Constraints

-l <string>
    input Texture Corpus Callosum Pole

-r <string>
    input Texture Poles

-c <FLOAT>
    Max difference stop criterium for the diffusion process ( default = 1e-6 )

-d <FLOAT>
    Iterative step ( default = 0.2 )

-b <S32>
    Context (in order to swap 0/360 around central sulcus if necessary)

-f <S32>
    process choice : 1 latitude only 2 longitude only 3 none 0 latitude and
    longitude

-t <FLOAT>
    data-driven weight

-a <S32>
    Beta Map (1=Yes, 0=No)

-x <string>
    output Latitude Texture

-y <string>
    output Longitude Texture

[ --insula <boolean> ]
    do parameterize insula

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsCorticalThickness


    AimsCorticalThickness
    ---------------------

AimsMeshMedianSurface

Options :

-i <string>
    White Hemisphere Mesh

-e <string>
    Grey/CSF Hemisphere Mesh

[ -v <string> ]
    Neighbours table file (from "arrival" mesh)

-d <U32>
    Process direction (int -> ext || ext -> int)

[ -vout <string> ]
    Output file in case the neighbours table would not be available and should
    be computed (6th order by default)

[ -o <string> ]
    Output width texture

[ -v2 <string> ]
    [DEBUG ONLY] Neighbours table file (from "other arrival" mesh)

[ -m <string> ]
    If provided, saves the created median mesh used for thickness computation

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsExactDepthArea


    AimsExactDepthArea
    ------------------

Compute the Exact Geodesic Depth Map

Options :

-im | --inputMesh <string>
    mesh

-it | --inputTexContour <string>
    input texture (contour area)

-ot | --inputTexDepth <string>
    output texture (depth map)

-v | --inputValue <S32>
    texture value contour

[ -c | --constraint <S32> ]
    constraintType:
    "0" -> no constraint
    "1" -> constrained sulci
    "2" -> constrained gyri
    "3" -> Exact geodesic path
    "4" -> Euclidian distance
    "5" -> z value

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsExtractGyrus


    AimsExtractGyrus
    ----------------

Extract a particular gyrus from a mesh and its gyri texture

Options :

-m | --mesh <string>
    input mesh

-t | --tex <string>
    gyri texture

-g | --gyrus <FLOAT>
    gyrus index

-lat | --latitude <string>
    latitude texture

-lon | --longitude <string>
    longitude texture

-o | --out <string>
    output gyrus name pattern

[ -dt <FLOAT> ]
    diffusion time step (default=0.01)

[ -delta <FLOAT> ]
    diffusion stoping criterion (default=0.0001)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsFlattenCortex


    AimsFlattenCortex
    -----------------

Create a flat representation of a cortical mesh if it has been parameterised

Options :

-m | --mesh <string>
    input mesh

-x | --xcoord <string>
    latitude texture

-y | --ycoord <string>
    longitude texture

-t | --tex <string>
    texture

-om | --outM <string>
    output mesh

-oi | --outI <string>
    output ima

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsFunctionProjection


    AimsFunctionProjection
    ----------------------

AimsFunctionProjection : first computes             anatomically-informed
kernels from one anatomy and uses them to project             some functional
data onto a cortical mesh

Options :

-op <S32>
    0 : computes convolution kernels from one anatomy ; 1 : projects functional
    volumes onto the surface (using kernels)

-m <string>
    Grey/white matter mesh (.mesh)

[ -d <string> ]
    Convolution kernels (.ima) to be used for projection (-op=1)

[ -d1 <string> ]
    4D functional volume (.ima/.img) to project onto the mesh (-op=1)

[ -i <S32> ]
    Size of computed kernels (integer)

[ -vx <FLOAT> ]
    X-resolution of kernels (float)

[ -vy <FLOAT> ]
    Y-resolution of kernels (float)

[ -vz <FLOAT> ]
    Z-resolution of kernels (float)

[ -g <FLOAT> ]
    Geodesic decay (in mm;default = 5.0) 

[ -n <FLOAT> ]
    Normal decay (in mm;default = 2.0)

[ -t <S32> ]
    For computing convolution kernels (-op=0), selects the cortical thickness
    evaluation method : 0 for 3mm constant (only for now) 

-o <string>
    Output file : convolution kernels (-op=0) or projection texture (-op=1)

[ -I <S32> ]
    [DEBUG] Index of a precise kernel to be computed

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsGeodesicPath


    AimsGeodesicPath
    ----------------

Compute the shortest path between two vertex

Options :

-i | --input <string>
    mesh

-s | --source <U32>
    index of source vertex

-t | --target <U32>
    index of target vertex

-o | --output <string>
    output file without extension file specified (.tex or .mesh)

[ -c | --constraint <S32> ]
    constraintType:
    "0" -> no constraint
    "1" -> constrained sulci
    "2" -> constrained gyri
    "3" -> Exact geodesic path

[ -st | --strain <S32> ]
    strain parameter (3 by default)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsGroupGyri


    AimsGroupGyri
    -------------

Group some of the original cortical gyri to get a new gyri model.

Options :

-m | --mesh <string>
    input mesh

-i | --in <string>
    input gyri texture

-o | --out <string>
    output gyri texture

-g | --grouping <string>
    grouping model file

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsGyriRegularization


    AimsGyriRegularization
    ----------------------

Build a regularized version of gyri from the 2D coordinate system. TEXTURE MUST
BE IN FLOAT !!!

Options :

-m | --mesh <string>
    input mesh

-i | --in <string>
    input gyri texture

-o | --out <string>
    output gyri texture

[ -w | --weight <FLOAT> ]
    data-driven term weight

[ -a | --anneal <S32> ]
    annealing (0=no, ICM; 1=yes

[ -s | --smooth <S32> ]
    Smoothing of probability maps (default=80)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsGyriStuff


    AimsGyriStuff
    -------------

Creation de gyri utilisant le systeme de coordonnees surfacique
AimsCorticalReferential

Options :

-x | --inLon <string>
    input Longitude Texture

-y | --inLat <string>
    input Latitude Texture

-a | --inCor <string>
    input Correspondance File

-o | --outTex <string>
    output texture

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsInterpolateVolumeToSurface


    AimsInterpolateVolumeToSurface
    ------------------------------

Projection d'un volume sur une surface par interpolation des noeuds de la
surface dans le volume 

Options :

-im | --inMesh <string>
    input Mesh

-iv | --inVol <string>
    input Volume

-o | --outTex <string>
    output Texture

-t | --type <S32>
    type d'interpolation (default: 0=trilinŽaire, 1=plus proche voisin

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshCoordinatesToDecimated


    AimsMeshCoordinatesToDecimated
    ------------------------------

Transfer 2D coordinates of a mesh to a decimated version of this mesh

Options :

-i | --input <string>
    input mesh

-d | --deci <string>
    decimatedMesh

-ix | --inputx <string>
    input x coordinate

-iy | --inputy <string>
    input y coordinate

-ox | --outputx <string>
    output x coordinate

-oy | --outputy <string>
    output y coordinate

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshIsoLine


    AimsMeshIsoLine
    ---------------

Create an isoline mesh (tube) for a textured mesh

Options :

-i | --inputMesh <string>
    input mesh

-t | --inputTex <string>
    input texture (TimeTexture<float>)

-o | --output <string>
    output mesh

-v | --value <S32>
    value of the isoline

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshMedianSurface


    AimsMeshMedianSurface
    ---------------------

AimsMeshMedianSurface

Options :

-i <string>
    White Hemisphere Mesh

-e <string>
    Grey/CSF Hemisphere Mesh

[ -v <string> ]
    Neighbours table file (from "arrival" mesh)

-d <U32>
    Process direction (int -> ext || ext -> int)

[ -vout <string> ]
    Output file in case the neighbours table would not be available and should
    be computed (8th order by default)

[ -o <string> ]
    Output mesh

[ -v2 <string> ]
    [DEBUG ONLY] Neighbours table file (from "other arrival" mesh)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshToAtlas


    AimsMeshToAtlas
    ---------------

Remesh a surface to a template atlas using spherical parameterization of both.
x-coordinate is the longitude (with a period). The atlas and the resulting mesh
then have a node to node correspondance

Options :

-i | --inputMesh <string>
    input mesh

-o | --outputTex <string>
    output mesh

-a | --atlasMesh <string>
    atlas mesh

-ix <string>
    mesh x-coordinate texture

-iy <string>
    mesh y-coordinate texture

-ax <string>
    atlas x-coordinate texture

-ay <string>
    atlas y-coordinate texture

-px <FLOAT>
    x-coord period (none=0)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsMeshToMeshPoint


    AimsMeshToMeshPoint
    -------------------

From a point on a mesh find the closest point on another mesh

Options :

-m1 | --mesh1 <string>
    source mesh

-m2 | --mesh2 <string>
    target mesh

-p | --point <U32>
    point index on source mesh

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsParameterizeGyri


    AimsParameterizeGyri
    --------------------

Paramétrisation de la surface corticale à partir d'une parcellisation en gyri

Options :

-i | --inMesh <string>
    inputMesh

-t | --inTex <string>
    gyral parcellation inputTexture

-g | --gyri <string>
    gyri to texture correspondance table

-m | --model <string>
    text file model of the relations between gyri and the system constraints

[ -s | --spmtex <string> ]
    activation texture for surface-based mapping ( default = "" )

-c | --constraint <U32>
    constraint method (0 = w/o constraints, 1 = iso-extracted constraints, 2 =
    mixed constraints, 3 = functional constraints iso-extracted mode, 4 =
    functional constraints mixed mode, 5 = spot constraints)

[ -C | --criter <FLOAT> ]
    Limit for the diffusion process ( default = 1e-4 )

[ -d | --dt <FLOAT> ]
    Iterative step ( default = 0.05 )

-o | --outTex <string>
    outputTexture

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsParameterizeSulcus


    AimsParameterizeSulcus
    ----------------------

Parameterize the mesh of a sulcus

Options :

-i | --input <string>
    input mesh

-b | --bottom <string>
    sulcus bottom point image

-t | --top <string>
    sulcus top point (junction with brain hull) image

-o | --orientation <S32>
    sulcus main orientation : top->bottom = 0, back->front = 1

-ox | --outputx <string>
    1st output texture (depth)

-oy | --outputy <string>
    2nd output texture ('along' the sulcus)

[ -m | --method <string> ]
    curvature computation method (fem/boix/barycenter, default=boix)

[ -d | --deltaT <FLOAT> ]
    diffusion iteration step (default=0.05)

[ -s | --stop <FLOAT> ]
    laplacian variation stopping criterion (default=0.000003)

[ -di | --dilation <S16> ]
    dilation of the ridges (1=yes (default), 0=no)

-mo <FLOAT>
    Morphological offset between dilation and erosion of ridges for extrem
    cases (default=0, otherwise should be 1.0)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsPlotCoordinatesOnMesh


    AimsPlotCoordinatesOnMesh
    -------------------------

Plot a point defined by 2D coordinates by creating a texture

Options :

-i | --inputMesh <string>
    input mesh

-l | --lat <string>
    latitude texture

-L | --lon <string>
    longitude texture

-x | --plat <FLOAT>
    point latitude

-y | --plon <FLOAT>
    point longitude

-o | --outT <string>
    output texture

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsPlotOnSPhericalAtlas


--------------------------------------------------------------------------
AimsPlotOnSphericalAtlas  -i[nput]  <coordinates file>                    
                          -m        <atlas mesh>                          
                          -u        <longitude texture>                   
                          -v        <latitude texture>                    
                          -o        <output mesh>                         
                         [-h[elp]]                                        
                                                                          
 coordinate file (ASCII) contains one line per point, each line           
 contains only longitude and latitude separated by a space :              
                                                                          
 u1 v1                                                                    
 u2 v2                                                                    
 u3 v3                                                                    
 ...                                                                      
--------------------------------------------------------------------------

AimsSulcalLines


    AimsSulcalLines
    ---------------

Cortical Sulcal Lines (for cortical surface coordinate system)

Options :

-i | --inMesh <string>
    input Mesh

[ -m | --inMethod <S32> ]
    extraction of extremities method :
    1 : projection crop by basins 
    2 : map of probability (embc11 method)
    3 : 	map of density (NeuroImage method, by default) 
    4 : mGPDM (miccai) 
    5 : map of probability (basin user defined) : 

[ -o | --inSulcalines <string> ]
    output sulcal lines texture (.tex)

[ -c | --inTexCurv <string> ]
    input Texture Curvature (barycenter curvature by default)

[ -d | --inTexGeoDepth <string> ]
    input Texture Geodesic Depth

[ -t | --inConstraint <S32> ]
    constraint type (shortest path) :
    1 : on curvature map (by default)
    2 : on depth map

[ -st | --strain <S32> ]
    strain parameter (15 by default)

[ -b | --bottom <string> ]
    sulcus bottom point volume

[ -lb | --inLabelBasins <string> ]
    input label of basins (.txt)

[ -ls | --inLabelSulcalines <string> ]
    input file : label-constraint correspondances of Sulcalines (.txt)

[ -ct | --curvthresh <FLOAT> ]
    curvature threshold for basins segmentation (0.0 by default)

[ -s | --save <string> ]
    folder path for save texture

[ -si | --side <string> ]
    side of hemisphere (left, right, both)

[ -sb | --size_basins <FLOAT> ]
    threshold of basins size (50 by default)

[ -cv | --constraintvalue <S32> ]
    constraint value :
    1 Basin (by default) :
    2 LatLon value

[ -e | --max_extremities <S32> ]
    max number of extremities (2 by default)

[ -p <vector of FLOAT> ]
    threshold of probability (0.4 by default)

[ -lon | --inTexLon <string> ]
    input Texture Longitude Constraints

[ -lat | --inTexLat <string> ]
    input Texture Latitude Constraints

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSulcusCorticalSnake


    AimsSulcusCorticalSnake
    -----------------------

Project an entire sulcus using multi-scale snake

Options :

-i | --input <string>
    input constraint texture

-m | --mesh <string>
    hemisphere mesh

-v | --value <FLOAT>
    value of the constraint

-a | --alpha1 <FLOAT>
    Constraint distance parameter

-b | --alpha2 <FLOAT>
    curvature parameter

-c | --alpha3 <FLOAT>
    elasticity parameter

-o | --output <string>
    output texture

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsSulcusNormalizeDepthProfile


    AimsSulcusNormalizeDepthProfile
    -------------------------------

Compute depth and profile curve from SC 

Options :

-m | --mesh <string>
    input mesh

-x | --xcoord <string>
    x coordinate texture

-y | --ycoord <string>
    y coordinate texture

-d | --dist <string>
    dist to plan file

-o | --out <string>
    output text file

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsTextureCompare


    AimsTextureCompare
    ------------------

Compute the Hausdorff distance between two curves

Options :

-im | --inputMesh <string>
    mesh

-itS | --inputTexSource <string>
    input texture source

-itT | --inputTexTarget <string>
    input texture target

-v | --inputValue <S32>
    input texture value

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsTextureToAtlas


    AimsTextureToAtlas
    ------------------

Projet a texture from one mesh onto an atlas using spherical parameterization
of both. x-coordinate is the longitude (with a period)

Options :

-i | --inputMesh <string>
    input mesh

-t | --inputTex <string>
    input texture (float)

-o | --outputTex <string>
    output texture

-a | --atlasMesh <string>
    atlas mesh

-ix <string>
    mesh x-coordinate texture

-iy <string>
    mesh y-coordinate texture

-ax <string>
    atlas x-coordinate texture

-ay <string>
    atlas y-coordinate texture

-px <FLOAT>
    x-coord period (none=0)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


PlotFociForValidation


    PlotFociForValidation
    ---------------------

Plot a set of foci on a surface, from node indexes or coordinates, and compute
stats on their dispersion in the 2D space

Options :

-i | --input <string>
    input mesh

-o | --outut <string>
    output texture

-f | --foci <string>
    foci file

-m | --mode <U32>
    mode : 0=from indexes, 1=from coordinates

[ -x | --xcoord <string> ]
    latitude texture

[ -y | --ycoord <string> ]
    longitude texture

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


surfStructuralAnalysis


    surfStructuralAnalysis
    ----------------------

Initialize

Options :

-p | --primal <string>
    PS graph

[ -o | --output <string> ]
    PS graph

--run <S32>
    run

--save <U32>
    save

[ --verbose <S32> ]
    verbose

[ --ddw <FLOAT> ]
    ddweight

[ --ipsw <FLOAT> ]
    intrapsweight

[ --simw <FLOAT> ]
    simweight

[ --lsw <FLOAT> ]
    lsweight

[ --ddx1 <FLOAT> ]
    ddx1

[ --ddx2 <FLOAT> ]
    ddx2

[ --ddh <FLOAT> ]
    ddh

--energypath <string>
    energypath

--recuitpath <string>
    recuitpath

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


surfTexActivationSimulation


    surfTexActivationSimulation
    ---------------------------

surfTexActivationSimulation

Options :

-m <file name (read only): Mesh of VOID>
    mesh for testGeomap 

-o <string>
    output File

[ -n <FLOAT> ]
    bruit de fond

[ -l <FLOAT> ]
    bruit de position

[ -i <FLOAT> ]
    bruit d'intensité

[ -s <FLOAT> ]
    lissage

[ -F <vector of U64> ]
    vertex index list

[ -I <vector of U64> ]
    intensities

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


AimsPETInjectedDoseNormalize


    AimsPETInjectedDoseNormalize
    ----------------------------

PET data conversion to %ID/cc and %ID/g (SUV)

Options :

-i <string>
    Input PET image to be normalized

-o <string>
    PET image after radioactive decay correction 

[ -p <string> ]
    PET image after conversion to %ID/cc or %ID/g (if --suv and weight is
    given)

-tinj <FLOAT>
    Time of injection [in min]

-ttop <FLOAT>
    Time of top camera [in min]

[ -tser <FLOAT> ]
    Time of measured full serynge [in min]

[ -tempty <FLOAT> ]
    Time of measured empty serynge [in min]

[ -aser <FLOAT> ]
    Activity of full serynge [in µCi]

[ -aempty <FLOAT> ]
    Activity of empty serynge [in µCi]

[ --suv <boolean> ]
    Compute SUV

[ -weight <S32> ]
    Subject's weight [in g]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


BsiBSI


    BsiBSI
    ------

Calculation of volumes atrophy in the hippocampus with Boundary Shift Integral
(BSI).

Options :

--base <string>
    base input short data volume is file <filebase>

--repeat <string>
    repeat input short data volume is file <filerepeat>

-b <string>
    boundary input short data volume is file <fileboundary>

--inter <string>
    intersection, between segmentation, input short data volume is file
    <fileinter>

[ --mask <string> ]
    mask optionnal input short data volume is file <filemask>

[ --BSI <string> ]
    BSI result optionnal input short data volume is file <fileBSI> 

--BSItxt <string>
    txt file for BSI result optionnal input short data volume is file
    <fileBSItxt>

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)

bin/BsiBSI: user interruption

BsiDiffMask


    BsiDiffMask
    -----------

Difference between Input and Compared on a mask.

Options :

-i <string>
    input short data volume is file <filein>

-c <string>
    compared short data volume is file <filecomp>

-m <string>
    short data volume with mask for input data is file <filemask>

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)

bin/BsiDiffMask: user interruption

BsiNormIntensity


    BsiNormIntensity
    ----------------

Intensity normalisation for coupled segmentation from SPM values.

Options :

-b <string>
    input short data volume for base is file <fileBase>

-r <string>
    input short data volume for repeat is file <fileRepeat>

--intcb <string>
    intensity characteristics for base in <fileIntcBase>

--intcr <string>
    intensity characteristics for repeat in <fileIntcRepeat>

--nb <string>
    normalised short data volume for base is file <fileNBase>

--nr <string>
    normalised short data volume for repeat is file <fileNRepeat>

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)

bin/BsiNormIntensity: user interruption

ylAdvectEuclidean


    ylAdvectEuclidean
    -----------------

Advect a line from each voxel, keeping track of its length.

Options :

--domain <file name (read only): VolumeRef of S16>
    mask of the advection domain: one inside, zero outside

[ --seeds | --advect-domain <file name (read only): VolumeRef of S16> ]
    mask of the advection seeds - default: same as domain

[ --grad-field <file name (read only): VolumeRef of FLOAT> ]
    scalar field whose gradient is to be advected along

[ --fieldx <file name (read only): VolumeRef of FLOAT> ]
    x component of vector field to advect along

[ --fieldy <file name (read only): VolumeRef of FLOAT> ]
    y component of vector field to advect along

[ --fieldz <file name (read only): VolumeRef of FLOAT> ]
    z component of vector field to advect along

--output-length <filename: VolumeRef of FLOAT>
    output volume containing the advection distance

[ --step-size | --step <FLOAT> ]
    size of the advection step (millimetres) [default: 0.03]

[ --max-dist <FLOAT> ]
    maximum advection distance (millimetres) [default: 6]

[ --domain-type <string> ]
    interpolation type for the domain: boolean, interpolated, [default:
    interpolated]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


ylAdvectPath


    ylAdvectPath
    ------------

Advect a line from each voxel, recording advection tracts in a wireframe mesh.

Options :

--domain <file name (read only): VolumeRef of S16>
    mask of the advection domain: one inside, zero outside

[ --seeds | --advect-domain <file name (read only): VolumeRef of S16> ]
    mask of the advection seeds - default: same as domain

[ --grad-field <file name (read only): VolumeRef of FLOAT> ]
    scalar field whose gradient is to be advected along

[ --fieldx <file name (read only): VolumeRef of FLOAT> ]
    x component of vector field to advect along

[ --fieldy <file name (read only): VolumeRef of FLOAT> ]
    y component of vector field to advect along

[ --fieldz <file name (read only): VolumeRef of FLOAT> ]
    z component of vector field to advect along

--output-path <filename: Segments of VOID>
    output mesh containing the advection paths

[ --step-size | --step <FLOAT> ]
    size of the advection step (millimetres) [default: 0.03]

[ --max-dist <FLOAT> ]
    maximum advection distance (millimetres) [default: 6]

[ --domain-type <string> ]
    interpolation type for the domain: boolean, interpolated, [default:
    interpolated]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


ylAdvectTubes


    ylAdvectTubes
    -------------

Advect a tube from each voxel, keeping track of its volume and end surface.

Options :

--domain <file name (read only): VolumeRef of S16>
    mask of the advection domain: one inside, zero outside

[ --seeds | --advect-domain <file name (read only): VolumeRef of S16> ]
    mask of the advection seeds - default: same as domain

[ --grad-field <file name (read only): VolumeRef of FLOAT> ]
    scalar field whose gradient is to be advected along

[ --fieldx <file name (read only): VolumeRef of FLOAT> ]
    x component of vector field to advect along

[ --fieldy <file name (read only): VolumeRef of FLOAT> ]
    y component of vector field to advect along

[ --fieldz <file name (read only): VolumeRef of FLOAT> ]
    z component of vector field to advect along

--divergence <file name (read only): VolumeRef of FLOAT>
    divergence of the normalized vector field

--output-volumes <filename: VolumeRef of FLOAT>
    output volume containing the tubes' volume

--output-surfaces <filename: VolumeRef of FLOAT>
    output volume containing the tubes' end surface

[ --step-size | --step <FLOAT> ]
    size of the advection step (millimetres) [default: 0.03]

[ --max-dist <FLOAT> ]
    maximum advection distance (millimetres) [default: 6]

[ --domain-type <string> ]
    interpolation type for the domain: boolean, interpolated, [default:
    interpolated]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


ylAdvectValues


    ylAdvectValues
    --------------

Advect a line from each voxel, copying the destination label into each origin
voxel.

Options :

--domain <file name (read only): VolumeRef of S16>
    mask of the advection domain: one inside, zero outside

[ --seeds | --advect-domain <file name (read only): VolumeRef of S16> ]
    mask of the advection seeds - default: same as domain

[ --grad-field <file name (read only): VolumeRef of FLOAT> ]
    scalar field whose gradient is to be advected along

[ --fieldx <file name (read only): VolumeRef of FLOAT> ]
    x component of vector field to advect along

[ --fieldy <file name (read only): VolumeRef of FLOAT> ]
    y component of vector field to advect along

[ --fieldz <file name (read only): VolumeRef of FLOAT> ]
    z component of vector field to advect along

--seed-values <file name (read only): { Volume of FLOAT, Volume of S16 }>
    volume containing the values to be advected

--output-values <string>
    output volume containing the advected values

[ --step-size | --step <FLOAT> ]
    size of the advection step (millimetres) [default: 0.03]

[ --max-dist <FLOAT> ]
    maximum advection distance (millimetres) [default: 6]

[ --domain-type <string> ]
    interpolation type for the domain: boolean, interpolated, [default:
    interpolated]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


ylIsoCurvature


    ylIsoCurvature
    --------------

Compute the curvature of isosurfaces

Options :

--input | -i <file name (read only): VolumeRef of FLOAT>
    input image volume (scalar field)

--mode | -m <string>
    type of curvature to compute (mean, sum, geom, pri1, pri2)

--output | -o <filename: VolumeRef of FLOAT>
    output image volume containing the curvature of the isosurfaces of the
    input field

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


ylLabelEachVoxel


    ylLabelEachVoxel
    ----------------

Assign a unique label to each voxel of a mask.

Non-zero voxels of the mask are each assigned a positive unique label.

Options :

--input | -i <file name (read only): VolumeRef of S16>
    input mask

--output | -o <filename: VolumeRef of S32>
    output label volume with S32 datatype

[ --first | --first-label <S32> ]
    assign labels starting with this value [default: 1]

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


ylLaplacian


    ylLaplacian
    -----------

Solve the Laplacian model in the cortex

Options :

--classif | -i | --input <file name (read only): VolumeRef of S16>
    classification image of the cortex (100 inside, 0 in CSF, 200 in white
    matter)

--output | -o <filename: VolumeRef of FLOAT>
    output pseudo-temperature field (from 0 in CSF to 1 in the white matter)

[ --precision <FLOAT> ]
    desired maximum relative error in first-order finite differences (default:
    0.001)

[ --typical-cortical-thickness <FLOAT> ]
    typical thickness of the cortex (mm), used for accelerating convergence
    (default: 3mm)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


ylMakeTraversePseudoAreaMap


    ylMakeTraversePseudoAreaMap
    ---------------------------

Map the quality of cortex column regions

Options :

--input | -i <file name (read only): VolumeRef of S32>
    input label volume

--proj-csf <file name (read only): VolumeRef of FLOAT>
    projected coordinates of the CSF surface

--proj-white <file name (read only): VolumeRef of FLOAT>
    projected coordinates of the white surface

--classif <file name (read only): VolumeRef of S16>
    grey/white/CSF classification image

[ --goal-diameter <FLOAT> ]
    goal region diameter (in millimetres) [default: 0.5]

--output | -o <filename: carto_volume of FLOAT>
    output quality map

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


ylMergeCortexColumnRegions


    ylMergeCortexColumnRegions
    --------------------------

Aggregate over-segmented cortex column regions

Options :

--input | -i <file name (read only): VolumeRef of S32>
    input label volume

--proj-csf <file name (read only): VolumeRef of FLOAT>
    projected coordinates of the CSF surface

--proj-white <file name (read only): VolumeRef of FLOAT>
    projected coordinates of the white surface

--classif <file name (read only): VolumeRef of S16>
    grey/white/CSF classification image

[ --goal-diameter <FLOAT> ]
    goal region diameter (millimetres) [default: 0.5]

--output | -o <filename: VolumeRef of S32>
    output label volume

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


ylPropagateAlongField


    ylPropagateAlongField
    ---------------------

Propagate regions down a vector field

From all voxels of the seed volume that have the target label, the field
is followed in fixed-size steps until a seed is reached, or the maximum
number of iterations is exceeded.

Options :

--seeds <string>
    volume of labels (either S16 or S32):
    - positive labels are seeds,
    - zero is the region of propagation,
    - negative labels are forbidden regions.

[ --grad-field <file name (read only): VolumeRef of FLOAT> ]
    scalar field whose gradient is to be advected along

[ --fieldx <file name (read only): VolumeRef of FLOAT> ]
    x component of vector field to advect along

[ --fieldy <file name (read only): VolumeRef of FLOAT> ]
    y component of vector field to advect along

[ --fieldz <file name (read only): VolumeRef of FLOAT> ]
    z component of vector field to advect along

[ --target-label <S32> ]
    voxels having this label are used as starting points [default: 0]

[ --step <FLOAT> ]
    size of the advection step (millimetres) [default: 0.03]

[ --max-iter <U32> ]
    abort after so many iterations [default: 1000]

--output <string>
    output the propagated regions

[ --dest-points <filename: VolumeRef of FLOAT> ]
    output the destination points for each propagated voxel

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)


ylUpwindDistance


    ylUpwindDistance
    ----------------

Compute the distance to a boundary along the gradient of a scalar field.

Options :

--domain <file name (read only): volume of S16>
    label image defining the computation domain

--field <file name (read only): volume of FLOAT>
    scalar field whose gradient is used as the integration direction

[ --invert <boolean> ]
    work on inverted field (downfield instead of upfield)

[ --speed-map <file name (read only): VolumeRef of FLOAT> ]
    speed map of the field evolution (UNIMPLEMENTED)

[ --opposite-speed <boolean> ]
    use -1 * the speed map

--output <filename: VolumeRef of FLOAT>
    output volume containing the distance

[ --domain-label <S16> ]
    label of the propagation domain (default: 100)

[ --origin-label <S16> ]
    label of the origin object (default: 0)

[ --output_4d_volumes <S32> ]
    Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
    volume, no value = use .aimsrc configuration files)

[ --debugLevel <S32> ]
    Set debug information level (default = 0)

[ --verbose [ <S32> ] ]
    Set verbosity level (default = 0, without value = 1)

[ -h | --help <boolean> ]
    show help message

[ --version <boolean> ]
    show Cartograph version

[ --info <boolean> ]
    show libraries information (install, plugins, paths, etc.)

[ --optionsfile <string> ]
    Read additional commandline options from the specified file (one switch or
    value per line)