Commands help
brainvisa-cmake
aims-free
anatomist-free
anatomist-gpl
highres-cortex
morphologist-nonfree
morphologist-baby
sulci-nonfree
morphologist-ui
brainrat-private
bioprocessing
primatologist-gpl
constellation-nonfree
cortical_surface-nonfree
disco
brainvisa-cmake
aims-free
anatomist-free
anatomist-gpl
highres-cortex
morphologist-nonfree
morphologist-baby
sulci-nonfree
morphologist-ui
brainrat-private
bioprocessing
primatologist-gpl
constellation-nonfree
cortical_surface-nonfree
disco
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: /casa/host/build/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.
-r REMOVE_UNDER, --remove-under=REMOVE_UNDER
remove destination directories under the given
directory before copying new files in them. Multiple
-r options allowed.
-d REMOVE_DIR, --remove-dir=REMOVE_DIR
remove destination directories which are equal to the
given directory before copying new files in them.
Multiple -d options allowed.
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
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.
* status: Display a summary of the status of all source repositories.
* 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
="/casa/host/conf/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)
--def, --only-if-default
apply only steps which are defined as default steps in
the bv_maker.cfg config file. Equivalent to passing
--only-if-default to every substep which supports it.
-v, --verbose show as much information as possible
--version show bv_maker (brainvisa-cmake) version number
bv_nobadlink
/casa/host/build/bin/bv_nobadlink [directory1 [directory2 [...]]]:
recursively remove dead links in the given directories (default: current directory)
bv_sip4make
Usage:
sip [-h] [-V] [-a file] [-b file] [-B tag] [-c dir] [-d file] [-D] [-e] [-f] [-g] [-I dir] [-j #] [-k] [-m file] [-n name] [-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]
-D generate code for a debug build of Python
-e enable support for exceptions [default disabled]
-f warnings are handled as errors
-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]
-n name the qualified name of the private copy of the sip module
-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
-y file the name of the .pyi stub file [default not generated]
-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_svn_to_git
usage: Convert some svn repositories to git [-h] [-u] [-p PROJECT] [-r REPOS]
[-s SVN] [-A AUTHORS_FILE]
[--latest-release-version LATEST_RELEASE_VERSION]
[--p4 P4] [-g GRAFT]
options:
-h, --help show this help message and exit
-u, --update update projects instead of cloning them
-p PROJECT, --project PROJECT
project (component) to be converted. A project or
component name may precise which sub-directory in the
svn repos they are in, using a ":", ex: "soma-
base:soma/soma-base". If not specified, the project
dir is supposed to be found directly under the project
name directory in the base svn repository.Multiple
projects can be processed using multiple -p arguments
-r REPOS, --repos REPOS
git local repository directory [default: current
directory]
-s SVN, --svn SVN svn repository base URL [default:
https://bioproj.extra.cea.fr/neurosvn]
-A AUTHORS_FILE, --authors-file AUTHORS_FILE
authors file passed to git-svn: Syntax is compatible
with the file used by git cvsimport: loginname = Joe
User <user@example.com>
--latest-release-version LATEST_RELEASE_VERSION
version number (without the v prefix) of the Git tag
which will be created from the latest_release SVN tag
--p4 P4 convert old perforce directory project, to graft
missing history from. format:
project[:svn_dir[:git_dir]]]. Several -o options
allowed.
-g GRAFT, --graft GRAFT
graft the beginning of a project branch to the end of
another project branch to recover older history that
git-svn could not figure out (especially useful for
old perforce history). Several -g options allowed.
Syntax: later_project[/later_git_branch][@later_repos_
dir]:older_project[/older_git_branch][@older_repos_dir
]. Projects/branches should have been converted to git
first using -p / --p4 options (during this run of
bv_git_to_svn or a previous one). Ex:
axon/master:brainvisa/trunk will graft axon after
brainvisa. The default branches are resp. master and
trunk.
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.
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)
AimsApplyTransform
AimsApplyTransform
------------------
Apply a spatial transformation on an image, a mesh, a 'bucket'
(voxels list file), fiber tracts, a graph, or to points.
Depending on the type of input, the direct transformation and/or the
inverse transformation are needed:
- Images need the inverse transformation, because they are resampled
using pullback interpolation;
- Meshes and Bundles need the direct transformation only;
- Buckets and Graphs need the direct transformation (pushforward), but
a better interpolation method will be used for Buckets if the
inverse transformation is also available (combined pullback and
pushforward).
These rules apply for passing the transformations:
- An arbitrary number of transformations can be specified, they will
be composed in the order that they appear on the command line
(e.g. for flags '-m A.trm -m B.trm', A will be applied before B,
in other words, the matrix product BA will be used);
- Each transformation can be an affine transform (in .trm format) or
a displacement field (in .ima/.dim GIS format, a.k.a. "FFD" for
Free-Form Deformation);
- Direct transformations must be given with --direct-transform/-d/-m,
ordered from the input space to the target space;
- Inverse transformations must be given with --inverse-transform/-I/-M,
ordered from the target space to the input space;
- If only one transformation is specified (direct or inverse), the
other will be computed automatically if the full transformation
chain can be inverted. Otherwise, both transformation chains must
be specified completely.
The meaning of coordinates in the input image can be specified with
the --input-coords option. This option specifies how to interpret the
transformations contained in the image header. --input-coords can
take the following values:
- 'AIMS' (default): internal coordinate system of the AIMS library.
For images, this is defined as 'physical' coordinates in
millimetres, starting from zero at the centre of the rightmost,
most anterior, most superior voxel in the image. Note that AIMS
determines the anatomical orientation based on the header in a
format-dependent manner. For NIfTI it uses first qform then sform
if they point to a referential of known orientation, and falls back
to assuming a RAS+ on-disk orientation.
- 'auto': use the last transformation defined in the AIMS metadata
(i.e. the last or qform or sform to be defined) or fallback to
AIMS coordinates if no transformation is found.
- 'first': use the first transformation defined in the AIMS metadata,
i.e. the first or qform or sform to be defined.
- 'last': use the last transformation defined in the AIMS metadata,
i.e. the last or qform or sform to be defined.
- '0', '1'... or any non-negative integer: use the transformation
in that position (0-based) in the AIMS metadata field
'transformations' (0 is a synonym of 'first').
- a referential name or UUID: use that referential from the
'referentials' field of the AIMS image header, which is read from
the image header or the sidecar .minf file (the .minf takes
precedence). There are shortcuts for common cases:
- 'mni', or 'mni152': use MNI coordinates, which correspond to the
NIFTI_XFORM_MNI_152 intent, a.k.a. 'Talairach-MNI template-SPM',
in AIMS.
- 'scanner': use 'Scanner-based anatomical coordinates', which
correspond to the NIFTI_XFORM_SCANNER_ANAT intent.
- 'acpc': use the 'Talairach-AC/PC-Anatomist' referential.
- 'aligned': use the referential that corresponds to
the NIFTI_XFORM_ALIGNED_ANAT intent, a.k.a. 'Coordinates aligned
to another file or to anatomical truth' in AIMS.
- 'talairach': use the referential that corresponds to the
NIFTI_XFORM_TALAIRACH intent.
- 'NIFTI_XFORM_TEMPLATE_OTHER': use the referential that
corresponds to this intent ('Other template' in AIMS).
The header transformations of the output are set according to the
first rule that applies:
1. If --keep-transforms is passed, or if the applied transformation
is identity, the header transformations of the input object are
copied verbatim to the output. This mode should be used when
applying a corrective transformation.
2. If --reference is given and unless --ignore-reference-transform is
passed, the transformations of the reference object are copied to
the output.
3. If the applied transformation is affine, the output transformations
are set to the header transforms of the input, composed with the
applied transformation.
4. If none of the rules above apply, no transformations are set in
the output header.
Points mode is activated by passing the --points option.
In this mode, the --input option either specifies an ASCII file
containing point coordinates, or is directly one or several points
coordinates on the command-line. Points should be formatted as
"(x, y, z)", with parentheses and commas. Points will be written
to the output stream in the same format, one point per line.
The input or output file names can also be -, which means standard
input and standard output, respectively. If --output is omitted,
the points are written on standard output in a user-friendly format.
Note also that for meshes or points, the dimensions, voxel sizes,
reference, and resampling options are not needed and are ignored.
Options :
--input | -i <file name (read only): { Bucket of VOID, BundleMap of VOID, Graph
of VOID, Mesh of VOID, Mesh4 of VOID, Segments 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
[ --output | -o <string> ]
Output image
[ --direct-transform | -m | --motion | -d <vector of string> ]
direct transformation (from input space to output space). Multiple
transformations will be composed in the order that they are passed on the
command-line. The file name may be prefixed with 'inv:', in which case the
inverse of the transformation is used.
[ --inverse-transform | -I | -M <vector of string> ]
inverse transformation (from output space to input space). Multiple
transformations will be composed in the order that they are passed on the
command-line. The file name may be prefixed with 'inv:', in which case the
inverse of the transformation is used.
[ --input-coords <string> ]
How to interpret coordinates in the input image w.r.t. the transformations
written in the image header. See above. [default: AIMS]
[ --points <boolean> ]
Points mode: transform point coordinates (see above).
[ --interp | --type | -t <string> ]
Type of interpolation used for Volumes: n[earest], l[inear], q[uadratic],
c[cubic], quartic, quintic, six[thorder], seven[thorder], maj[ority],
med[ian] [default=linear]. Modes may also be specified as order number:
0=nearest, 1=linear... Additional values: 101=majority, 201=median
[ --background | --bg | -bv | --defaultvalue <string> ]
Value used for the background of Volumes
[ --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]
[ --reference | -r <string> ]
Volume used to define output voxel size and volume dimension (values are
overridden by --dx, --dy, --dz, --sx, --sy and --sz)
[ --keep-transforms <boolean> ]
Preserve the transformations of the input image
[ --ignore-reference-transforms <boolean> ]
Do not try to copy the transformations from the reference image
[ --vectorinterpolation | --vi <string> ]
Interpolation used for vector field transformations (a.k.a. FFD): l[inear],
c[ubic] [default = linear]
[ --mmap-fields <boolean> ]
Try to memory-map the deformation fields instead ofloading them entirely in
memory. This may improve the performance for transforming sparse point
sets.
[ --progress <string> ]
write progress info in this file. The file is opened in append mode, so
that it can be an existing file, already opened by a monitoring
application.
[ --vol_id <boolean> ]
When no tansform is specified (identity) and transformation applies between
volumes, then add a translation to compensate the difference in voxel sizes
between input and output geometries, and keep the same field of view
instead of the same origin. This is normally what we do when just changing
an image resolution.
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <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.
options:
-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
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]
[ -S <U64> ]
maximum 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): carto_volume of S16>
source matrix
-o | --output <filename: carto_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
---------------
3D curvature of an intensity image f(x,y) = I
Options :
-i | --input <file name (read only): carto_volume of S16>
source matrix
-o | --output <filename: carto_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
AimsDanielssonDist
------------------
Danielsson's 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
[ -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)
AimsDiff.py
usage: AimsDiff.py [-h] [--reader {AIMS,nibabel}] [--min-value MIN_VALUE]
[--max-value MAX_VALUE]
reference_file test_file
Compare two files read by AIMS and summarize the differences. Please note that
this program is intended for interactive use. The formatting of the output
should not be considered stable, it may be modified or extended in the future.
positional arguments:
reference_file reference data file
test_file test data file
options:
-h, --help show this help message and exit
--reader {AIMS,nibabel}
library used for reading the data (nibabel is
experimental)
--min-value MIN_VALUE
minimum value to be taken into account in comparisons
(smaller values are replaced by NaN internally
--max-value MAX_VALUE
maximum value to be taken into account in comparisons
(larger values are replaced by NaN internally
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)
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"
Absolute orientations can also be given in the 3 letters conventions ("RAS",
"LPI", etc, with L: axis toward Left side, R: right, A: anterior, P:
posterior, S: superior, I: inferior. Thus "RAS" is equivalent to "abs: -1
-1 -1", "LPI" is equivalent to "abs: 1 1 1" etc.
See: https://brainvisa.info/aimsdata/user_doc/coordinates_systems.html
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <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: 5.1]
[ --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)
/casa/host/build/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
-----------
Dump Gtm
Options :
-i | --input <string>
origin Roi file (arg format)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
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
AimsGraph2Volume.py
usage: Convert a ROI graph to a volume, following labels and colors in a hierarchical nomenclature: values used in the volume will not be the index in the graph, but the "label" value in the nomenclature: thus the nomenclature has to have this attribute for each region, and be a number.
If no nomenclature is provided, regions numbers will be generated in an arbitrary order
The output volume will have a labels table with colors in the header attribute "GIFTI_labels_table", as in Gifti textures.
[-h] [-i INPUT] [-n NOMENCLATURE] [-o OUTPUT] [-a ATTRIBUTE]
options:
-h, --help show this help message and exit
-i INPUT, --input INPUT
input graph
-n NOMENCLATURE, --nomenclature NOMENCLATURE
nomenclature (optional)
-o OUTPUT, --output OUTPUT
output volume
-a ATTRIBUTE, --attribute ATTRIBUTE
item attribute id (bucket attribute id in vertices).
Default: use the one available if only one is present
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
[ -n <string> ]
Output nomenclature (.hie) filename, converted from volume header
labels/colors table (GIFTI_labels_table)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <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: VolumeRef 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
options:
-h, --help show this help message and exit
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
----------------
Regularization of the tensor maps with a Spaghetti Markov Field
Options :
-i | --input <file name (read only): bucket of DTITENSOR>
bucket of dtitensor to be regularized
-o | --output <filename: bucket of DTITENSOR>
result of the regularization
[ -a | --alpha <FLOAT> ]
energy balancing [default=1.0]: V = V(spaghetti) + alpha x V(attachment)
[ -m | --modifAngle <FLOAT> ]
maximum angle in degrees between the direction of a neighbor of a voxel and
the spin of that voxel [default=45deg]
[ -n | --neighborAngle <FLOAT> ]
maximum angle in degrees beetween 2 spins to be considered in the same
fiber [default=46deg]
[ -s | --sampling <S32> ]
minimum number of discrete unit vectors uniformly distributed on a unit
sphere [default=100]
[ -M | --MaxIter <S32> ]
stop the ICM after a maximum number of iterations [default=30]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsIcmSpaghettiN
AimsIcmSpaghettiN
-----------------
Regularization of the tensor maps with a Spaghetti Markov Field
Options :
-i | --input <file name (read only): bucket of DTITENSOR>
bucket of dtitensor to be regularized
-o | --output <filename: bucket of DTITENSOR>
result of the regularization
[ -a | --alpha <FLOAT> ]
energy balancing [default=1.0]: V = V(spaghetti) + alpha x V(attachment)
[ -m | --modifAngle <FLOAT> ]
maximum angle in degrees between the direction of a neighbor of a voxel and
the spin of that voxel [default=45deg]
[ -n | --neighborAngle <FLOAT> ]
maximum angle in degrees beetween 2 spins to be considered in the same
fiber [default=46deg]
[ -s | --sampling <S32> ]
minimum number of discrete unit vectors uniformly distributed on a unit
sphere [default=100]
[ --neighbor <S32> ]
number of neighbor by semi-conic neighborhood [default=all]
[ -M | --MaxIter <S32> ]
stop the ICM after a maximum number of iterations [default=30]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsIcosaList
AimsIcosaList
-------------
Output a file with coordinates of discrete spheric distribution
Options :
-d | --direction <S32>
number of discrete directions
-o | --output <string>
output ASCII file
[ -e | --epsilon <FLOAT> ]
error on dot product (+d).(-d) [default=1e-6]
[ -a | --all <boolean> ]
all directions (+d and -d) (useful for DTI where +d and -d are equivalent
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
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)
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)
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)
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)
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]
[ -l <string> ]
Voxel value of the mask label [default=non null]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
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
----------------
3D Hamilton-Jacobi evolution of a binary short image f(x,y,z)
Fast tubular method - Mean Curvature Flow
Ut = - F1.K.||DU||
Options :
-i | --input <file name (read only): volume of S16>
input SHORT binary volume
-o | --output <string>
prefix name for output SHORT volumes
-e | --epoch <S32>
number of evolving iterations to proceed
[ -F | --F1 <FLOAT> ]
speed function F = F1.K [default F1=-1.0]
[ -t | --time <FLOAT> ]
time step in seconds [default=0.1]
[ -s | --step <S32> ]
number of time iterations between 2 backups [default=1]
[ -u | --uradius <FLOAT> ]
radius of the evolving tube [default=12]
[ -c | --curvature <Pc> ]
curvature type: mean, gaussian, mean-gaussian, min, max
[default=mean-gaussian]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
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 : /casa/host/build/bin/AimsMesh2Ascii filein.mesh fileout.txt
AimsMesh2SSGraph
/casa/host/build/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)
AimsMeshCleaner
(Compiled at 15:28:14 on Sep 1 2023)
Reading mesh...
AimsMeshCleaner
---------------
Remove points with high positive curvature
Points with negative curvature are left untouched.
Options :
-i <file name (read only): Mesh of VOID>
input mesh
-o <filename: Mesh of VOID>
output mesh
-maxCurv <FLOAT>
maximum unoriented (but signed) 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)
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, "gaussian" -> 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 for the tube
part (default: 1)
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 : parallelepiped
boundingbox_max : 3D position of the higher bounding box
boundingbox_min : 3D position of the lower bounding box
smooth : (optional) make smooth normals and shared vertices (default: 0)
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
options:
-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)
AimsNormWithRegion
AimsNormWithRegion
------------------
? - Anybody knows what this command does ?
Options :
-i | --input <file name (read only): volume of FLOAT>
dynamic series: input dynamic data
-o | --output <filename: volume of FLOAT>
norm image
-v | --voi <file name (read only): Graph>
voifile: ile containing roi information see(--voitype
-n | --name <string>
reference ROI name (from selectionlist)
[ -m | --motion <file name (read only): AffineTransformation3d> ]
displacement file default val : Identity
[ -l | --list <6Helper> ]
list of available template selectors
[ -d | --dose <FLOAT> ]
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
[ --hierarchy <file name (read only): Hierarchy> ]
hierarchyfile
[ --selection <string> ]
template selector: template selector name available selectors may be
listed (switch -l), or all to disable selection mode
[ -x <boolean> ]
nothing
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
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
-------------------
Correction of DTI distorsions from an existing parameter file
Options :
-d | --distorted <file name (read only): volume of S16>
source S16 distorded data
-o | --output <filename: volume of S16>
destination S16 data file name
-p | --parameter <string>
parameter file containing corrections
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
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)
AimsParcelsSurfaceFeatures.py
usage: Record surface parcel-level features (surface, boundary length) on a set of clusters textures
[-h] [-i INPUT] [-o OUTPUT] [-m MESH] [-a ATTRIBUTE]
options:
-h, --help show this help message and exit
-i INPUT, --input INPUT
input textures
-o OUTPUT, --output OUTPUT
output features (.json or .csv)
-m MESH, --mesh MESH input meshes
-a ATTRIBUTE, --attribute ATTRIBUTE
item attributes. Each -a item corresponds to an input
texture. Attributes will be stored in the features
file as index keys. A value here is parsed as a JSON
dict. A special key, "index" allows to use only the
specified timestep in the corresponding input texture
(otherwise all timesteps are used)
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
--------------------
In most cases you should rather use AimsApplyTransform instead of
AimsRegisterFFDApply. This command has been mostly replaced with the above one,
except for the -b, -g, -c and --old-mode options. So if you are not using these
options, use AimsApplyTransform preferably, which is more powerful, and clearer
to use.
Typically to deform an image, the equivalent to:
AimsRegisterFFDApply -i image.nii -o output.nii -d ffd.ima -m affine.trm
will be:
AimsApplyTransform -i image.nii -o output.nii -M inv:affine.trm -M ffd.ima --vi
3 -t 3
Apply FFD (vector field) transformation on an image, a mesh, a 'bucket' (voxels
list file), fiber tracts, a graph, or to points.
Note that when resampling an image, the transformations must represent the
inverse direction (for a destination point we seek the source position of the
point), but for meshes, buckets, fibers, or points the transformations are
applied directly (a vertex is moved according to the vector field). Similarly,
the transformations are applied in the order that they are passed on the
command-line. As a result:
- when resampling an image, inverse transformations must be given, ordered from
the target space to the input space. This also applies to affine
transformations (this is the opposite convention to AimsResample, use the :inv
suffix to invert affine transformations on the fly).
- when resampling meshes, buckets, fibers, or points, the direct
transformations should be given, ordered from the input space to the target
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, Mesh4 of VOID, Segments 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 | --transform <vector of string> ]
transformations to be applied. Multiple transformation will be composed in
the order that they are passed on the command-line. Affine transformations
may be suffixed with :inv to use their inverse.
[ -m | --motion <string> ]
Input affine transformation (deprecated: you can now pass affine
transformations with -d)
[ -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 a deformation field corresponding to the composed transformation
[ -c | --compression <string> ]
Output compression volume
[ --old-mode <boolean> ]
Make this command work with pre-2015 FFD motions (which are in voxels of
the input image, 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 any tool that you want
3. Feed the warped images 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 | -i <file name (read only): VolumeRef of FLOAT> ]
transformed multi-channel image of X, Y, and Z coordinates (4D or 5D)
[ --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
------------
This command is obsolete. Please use AimsApplyTransform instead. The same
options and arguments will just work in most cases, except for the "-d" option,
which should be replaced with "--bg" instead. This old command is now disabled,
unless the "--force" option is passed.
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> ]
Type of interpolation used: n[earest], l[inear], q[uadratic], c[cubic],
quartic, quintic, six[thorder], seven[thorder], maj[ority], med[ian]
[default=linear]. Modes may also be specified as order number: 0=nearest,
1=linear... Additional values: 101=majority, 201=median
[ -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]
[ --force <boolean> ]
force use of AimsResample despite its obsolescence (it will refuse to work
otherwise)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <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
------------------
Take a list of segments (pairs of points) and build a 3D composed of cylinders.
Each cylinder joins two points of a segment.
Options :
-i | --input <string>
Series of pairs of 3D points
-o | --output <filename: Mesh of VOID>
output mesh file
[ -w | --width <FLOAT> ]
Width of the cylinder (default 1)
[ -v | --verbose <S32> ]
display information on standard error output
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
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. The command can append, remove, or replace an existing
transformation in the input file. Note that some formats will force certain
transformations to exist or to respect certain criteria, such as the qform in
nifti files which should be rotation + translation only. In such a case it is
possible that the output file will contain some additional transformations
which are not "wanted" here (they are added by the IO layer upon writing).
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
-o OUTPUT, --output=OUTPUT
output object file name. Default: overwrite input
AimsSiemensEPI2Volume
AimsSiemensEPI2Volume
---------------------
Concatenates all Siemens NEMA EPI images to a 4D data file
Options :
-i | --input <string>
input file - its directory is actually used
-o | --output <filename: volume of S16>
output file
-f | --first <S32>
first image number in series
-s | --slices <S32>
number of slices
-r | --repetitions <S32>
number of repetitions
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
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)
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
-------------
Extracting a subpart from a DtiTensor bucket
Options :
-i | --input <file name (read only): bucket of DTITENSOR>
source tensor bucket
-o | --output <filename: bucket of DTITENSOR>
output bucket of sub-dtitensor
[ -x <S16> ]
inferior point of the box sub-part
[ -y <S16> ]
inferior point of the box sub-part
[ -z <S16> ]
inferior point of the box sub-part
[ -X <S16> ]
superior point of the box sub-part
[ -Y <S16> ]
superior point of the box sub-part
[ -Z <S16> ]
superior point of the box sub-part
[ -m | --mask <file name (read only): bucket of VOID> ]
Void bucket file 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)
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
Mesh4 of VOID
Segments 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)
AimsTensorExtract
AimsTensorExtract
-----------------
Extract anisotropy,trace,directions from dtitensor bucket
Options :
-i | --input <file name (read only): bucket of DTITENSOR>
source dtitensor bucket
[ -o | --output <string> ]
destination base file name, will be suffixed:fileout_traceTC.ima,
fileout_traceEV.ima, fileout_VR.ima, fileout_FA.ima, fileout_dir.ima,
fileout_dirRGB.ima. default=input file name
-x | --xdim <S32>
dimensions of output images
-y | --ydim <S32>
dimensions of output images
-z | --zdim <S32>
dimensions of output images
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsTensorSNR
AimsTensorSNR
-------------
SNR of a VOI in a tensor image
Options :
-i | --input <file name (read only): bucket of DTITENSOR>
dtitensor bucket file
[ -v | --voi <file name (read only): volume of U8> ]
U8 data file of the V.O.I.
[ -x <S16> ]
Point3d center of a spherical ROI
[ -y <S16> ]
Point3d center of a spherical ROI
[ -z <S16> ]
Point3d center of a spherical ROI
[ -R <FLOAT> ]
radius of spherical ROI
[ -o | --output <string> ]
output file [default=stdout]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
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
------------------
Build the primal sketch of a texture using 2D geodesic diffusion
Options :
-i | --input <file name (read only): texture of FLOAT>
input texture
-v | --volume <string>
input volume (used for size)
-M | --mesh <file name (read only): Mesh of VOID>
input mesh
-F | --flat_mesh <file name (read only): Mesh of VOID>
inflated mesh file
-B | --Blobs <filename: texture of S32>
output blobs texture
-o | --outputss <filename: texture of FLOAT>
output scalespace texture
-b | --beginscale <FLOAT>
First scale in the scale space
-e | --endscale <FLOAT>
Last scale in the scale space
-d | --dt <FLOAT>
Max sample step in the scale space
[ -g | --graph <filename: Graph> ]
output graph, (Grey Level Blob graph) <default = not used>
[ -p | --primal <filename: Graph> ]
output corresponding primal sketch graph (needs also -g) (Scale Space Blob
graph) <default = not used>
[ --log <boolean> ]
use log scale
[ -H | --Hmax <FLOAT> ]
(Absolute) threshold for the textures values <default = auto (max of the
texture)>)
[ -s | --surface <string> ]
surface_type: Tore (default) or surface
[ -G | --Grow <string> ]
Mesh growing mode along scales: scale (default), translate, or pushnormal
[ -t | --trans | --translation <FLOAT> ]
Link between the scale and the distance to the mesh
[ -m | --mindt <S32> ]
min scale space sample step: Min sample step in the scale space, <default =
scale space sample step>
[ -W | --Weightmax | --Wmax <FLOAT> ]
(Absolute) threshold for the laplacian weight estimate, <default = 0.1>
[ -S | --smoothstep <FLOAT> ]
Time step for te edp (depending from the triangulation), <default =
automatic>
[ -c | --convexity | --concavity <FLOAT> ]
Convexity: Grey level blob correspond to: * local minima (convexity = -1),
* local maxima (convexity = 1), <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)
AimsTextureAverage
AimsTextureAverage
------------------
Compute the average of a time-series texture
Options :
-f | --float_texture | -i <file name (read only): texture of FLOAT>
input time-series texture
-o | --output <filename: texture of FLOAT>
output mean texture
[ -b | --binary <boolean> ]
binarize the input texture
[ --max <boolean> ]
compute the maximum instead of the mean input texture
[ --min <boolean> ]
compute the minimum instead of the mean 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)
AimsTextureCleaning.py
usage: AimsTextureCleaning.py [-h] [-t [TEXTURE ...]] [-m [MESH ...]]
[-o [OUTPUT ...]] [-n NOMENCLATURE] [-e EROSION]
[-d DILATION] [-s MINSIZE] [-p PROC]
Clean parcellation textures (developed initially for JulichBrain projections).
Should normally be used after volume to texture projection using AimsVol2Tex.
The nomenclature is basically an int/string labels conversion table, but may
include colors in addition to build a consistent colormap. The nomenclature
file may be given in different formats: JSON, CSV, or HIE.
- JSON (JulichBrain nomenclature):
{"properties": {"regions": [<region_def>, ...]}}
region_def: { "labelIndex": "12", "name": "rototo", "color": [255, 255, 0],
"children": [<region_def>, ...] }
- CSV (JulichBrain nomenclature):
12, rototo
(all colors will be black)
- HIE (AIMS Hierarchical nomenclature)
- XML (JulichBrain niftis)
options:
-h, --help show this help message and exit
-t [TEXTURE ...], --texture [TEXTURE ...]
input textures
-m [MESH ...], --mesh [MESH ...]
input meshes
-o [OUTPUT ...], --output [OUTPUT ...]
output textures
-n NOMENCLATURE, --nomenclature NOMENCLATURE
nomenclature int->string table file (JSON, or CSV, or
HIE)
-e EROSION, --erosion EROSION
erosion distances dict to remove small parts. Default:
{'unknown': 7.0, 'GapMap': 1.5, 'other': 0.5}
-d DILATION, --dilation DILATION
dilation distance (mm) to connect disconnected
regions. Default: 1.500000
-s MINSIZE, --minsize MINSIZE
minimum disconnected component size (in mm2) under
which remaining small parts are removed. Default:
100.000000
-p PROC, --proc PROC Use parallel computing using this number of processors
(cores). 0=all in the machine, positive number=this
number of cores, negative number=all but this number.
Default: 0 (all)
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
-----------
apply a V-Filter to an image
Options :
-i | --input <file name (read only): volume of S16>
input file
-o | --output <filename: volume of S16>
output file
[ -m | --masksize <S32> ]
mask size [default=2]
[ -t | --type <Pc> ]
algo type: o -> optimized, n -> non optimized [default=o]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
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)
AimsVol2Tex
AimsVol2Tex
-----------
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 <FLOAT> ]
cylinder half height (mm) [default=1]
[ -int_height <FLOAT> ]
cylinder half height on interior side of the mesh (mm). Only used if
mode=4. [default=0]
[ -radius <FLOAT> ]
cylinder radius (mm) [default=1]
[ -mode <S32> ]
cylinder direction (1:interior, 2:exterior, 3:both, 4: both with differing
sizes) [default=3]
[ -b <file name (read only): carto_volume of S16> ]
brain mask file [default=no brain mask]. May be either a binary volume, or
a labels volume (regions): used together with the -p option, allows to
separate projected values in regions they belong to.
[ -v <S32> ]
value mode (0: majority (labels), 1: average, 2: max, 3: min, 4: median)
[ -p <file name (read only): carto_volume of S16> ]
projection texture. They can be used in two ways:
- binary mask on vertices: only vertices with a non-zero value will be
processed.
- labels map: together with a volume labels mask (-b option): values from
the input (-i) volume will be processed only if the label of the voxel (-b)
and of the projection texture (-p) match. A projection texture can be
obtained using a first run of AimsLabels2Tex, then used as input to a
second run using float data: it will thus mask each region to avoid mixing
values from different labelled regions.
[ --bg <FLOAT> ]
background value in the output texture (default: 0)
[ --maskbg <S16> ]
background value in the input masks (brain and projection texture, if any
(default: 0)
[ -a | --apply_to <string> ]
apply to values from this other input volume.
In min/max/median modes, take the min/max/median position for each cylinder
from the input volume, but take the output texture value in another volume
specified here. This option is not useful in average mode since in that
case it does not differ from using an optional mask and the input volume.
To be clearer we get for each cylinder the max position (for instance) of
input volume (-i) values, then get the output texture from this volume (-a)
at the same position.
The "majority" value mode does not use this additional volume.
The apply_to volume is converted into the same data type as the main input
volume.
[ -t | --transform <file name (read only): Transformation3d> ]
Optional transformation between the mesh and the volume (mesh to volume) -
any 3D transform is accepted including non-linear vector fields
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <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
/casa/host/build/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
/casa/host/build/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.) Note that now, AimsApplyTransform can resample
graphs and other object, in a better way than this mainly unmaintained command
- but without the label filtering, which is the reason we have not removed
this command.
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 . Image
(or other objects) can be named I1, I2... or image[1],
image[2] etc. Indices normally start at 1 (kind of
matlab-style) but can start at 0 if the -z option is
used. A formula is basically a python expression, thus
can use anything supported in python expressions. ex:
sum(images). Numpy may be used (as np), and numpy
results can be converted to volumes: np.asarray(I1) **
2, or np.sqrt(I1)
-i FILENAME, --input=FILENAME
input volume(s)
-l, --lazy use lazy reading and release of objects during the
formula evaluation. With this option, each image is
loaded when used, and released once one operation has
been performed with it. It allows to process large
lists of images without loading all of them in memory,
but will read them several times if they are used
several times in the formula. (see
aims.lazy_read_data.LasyReadData python class for
details)
-t THREADS, --threads=THREADS
use threaded preloading when iterating over the list
of images (see
soma.aims.lazy_read_data.PreloadIterator python class
for details). Implies -l, and only useful when using
an iteration over the list of volumes, such as in the
formula "sum(image)". In such an iteration volumes in
the later iterations can be preloaded using threads,
making the process much faster. The number of threads
/ preloads is specified with this option. 0 means
guess the number of CPUs of the current machine.
Default is 1: no thraading/preloading
-z, --zero start indexing images at index 0 (instead of 1 by
default): I0, I1 etc and image[0], image[1] etc.
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" ]
anatomist
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-brainvisa'
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.
mkhierarchy-anatomist
usage : /casa/host/build/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
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 : /casa/host/build/build_fil
es/axon/../../share/brainvisa-share-
5.1/nomenclature/translation/sulci_model_noroots.trl)
--hie=FILE hiearchy (default : /casa/host/build/build_files/axon/
../../share/brainvisa-share-
5.1/nomenclature/hierarchy/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)
ana_atlas_nonlin.py
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-brainvisa'
Starting Anatomist.....
config file : /casa/home/.anatomist/config/settings.cfg
global modules: /casa/host/build/build_files/axon/../../share/anatomist-5.1/python_plugins
home modules: /casa/home/.anatomist/python_plugins
loading module meshsplit
loading module modelGraphs
loading module histogram
loading module bundles_split_by_cortical_regions
loading module palettecontrols
loading module paletteViewer
loading module ana_image_math
loading module simple_controls
loading module bsa_proba
loading module selection
loading module bundles_small_brains
loading module anacontrolmenu
loading module gradientpalette
loading module foldsplit
loading module profilewindow
loading module save_resampled
loading module volumepalettes
loading module gltf_io
all python modules loaded
Anatomist started.
usage: /casa/host/build/bin/ana_atlas_nonlin.py [-h] [-s] [object_file ...]
Run Anatomist with a ROI navigation control with the following features: *
Linked cursor between windows with non-linear deformation fields: non-linear
transformations can be loaded between referentials which are not linked via
regulart affine transformations. Clicks coordinates are transformed and sent
to other windows. * ROI selection: selectionned objects (double-click) are
handled by their name/label, then all objects with the same name/label are
also selected in all views. Views are focused on the bounding box of the
selected objects. The specified objects are loaded at launch time, and any
.yaml file is interpreted as a transformations graph. Non-linear
transformations (vector fields) between MNI152 2009c asymmetric, Colin27,
BigBrain and an infant atlas templates can be downloaded from the Human Brain
Project (HBP) knowledge graph: https://search.kg.ebrains.eu/instances/Dataset/
7a9aa738-a5b2-4601-818e-05db2627ba5c A transformations graph (graph.yaml) is
also found in this dataset and may be passed to this program. The
corresponding atlases templates can be downloaded using the links there.
However to work correctly the template images have to be marked with the
correct referentials IDs. The ICBM152 template is already marked, but others
must be added a .minf file (text file): - for Colin27: create
colin27_t1_tal_lin.nii.minf: attributes = { "referentials": ["ID: MNI Colin
27"], } - for the BigBrain, the referential is "Big Brain (Histology)" - for
the infants template the referential is "Infant atlas"
positional arguments:
object_file Load objects or transformation graph (.yaml)
options:
-h, --help show this help message and exit
-s, --split use separate windows (default: use a views block)
PyAnatomist Module present
PythonLauncher::runModules()
Exiting Anatomist --- Goodbye.
Exiting QApplication
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
/casa/host/build/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)
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)
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
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]
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]]
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]
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
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]
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] {int (default : not used)}]
[-threshmode {abs (absolute), grey (31343065067f grey level peak), default: use grey peak - 3 sigma}]
[-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]
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]]
VipListLabel
Usage: VipListLabel
-i[mage] {image name}
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]]
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]
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
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: n, c or o (default:c)}]
Automatic estimation of the background intensity threshold
n: no estimation, default threshold at 15
c: 2004 version of the threshold estimation using the corners of the image
o: 2019 version of the threshold estimation using the otsu threshold
[-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]]
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
/casa/host/build/bin/neurlearn: invalid option -- 'h'
usage: /casa/host/build/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: /casa/host/build/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: /casa/host/build/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 :
/casa/host/build/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 : /casa/host/build/b
uild_files/axon/../../share/brainvisa-share-
5.1/nomenclature/translation/sulci_model_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
/casa/host/build/bin/siDisplayGraph.py:9: DeprecationWarning: Please use `BivariateSpline` from the `scipy.interpolate` namespace, the `scipy.interpolate.fitpack2` namespace is deprecated.
from scipy.interpolate.fitpack2 import BivariateSpline, dfitpack
/casa/host/build/bin/siDisplayGraph.py:9: DeprecationWarning: Please use `dfitpack` from the `scipy.interpolate` namespace, the `scipy.interpolate.fitpack2` namespace is deprecated.
from scipy.interpolate.fitpack2 import BivariateSpline, dfitpack
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 : /casa/host/build/build_fil
es/axon/../../share/brainvisa-share-
5.1/nomenclature/translation/sulci_model_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 :
/casa/host/build/bin/siDivNameList [-p prefix] n directory savefile
/casa/host/build/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 :
/casa/host/build/bin/siDomTrain paramFile
/casa/host/build/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 : /casa/host/build/build_fil
es/axon/../../share/brainvisa-share-
5.1/nomenclature/translation/sulci_model_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 :
/casa/host/build/build_files/axon/../../share/brainvis
a-share-
5.1/nomenclature/hierarchy/sulcal_root_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
/casa/host/build/bin/siGenerateLearningTasks.py:9: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
import distutils.spawn
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 : brainvisa,,,@cea.fr)
-p MODE, --parallelism-mode=MODE
['grid', 'duch', 'cath', 'LSF', '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 : /casa/host/build/build_fil
es/axon/../../share/brainvisa-share-
5.1/nomenclature/translation/sulci_model_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 :
/casa/host/build/bin/siLearn paramFile
/casa/host/build/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 :
/casa/host/build/bin/siLyxErrors resultfile.lyx resultfile.tre [dir]
dir: directory o� seront �crites les images .eps
Ecrit les tableaux d'erreurs dans un fichier au format LyX
Ces erreurs doivent avoir �t� calcul�es 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: 5.1]
[ --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
---------------------------
Make sulci and gyri hierarchy for parcellation
Options :
-g | --gyri <string>
output gyrus hierarchy
-s | --sulci <string>
output sulcus hierarchy
-l | --level <string>
level model: Choice of the level of description file ('*.trl')
-m | --model <string>
input gyri model: Choice of the sulcus/sulcus relations ('*.gyr')
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
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
-------------------
Give different measures related to the sulci operture and cortex thickness
Options :
-G | --grey | --white <file name (read only): Mesh of VOID>
input grey/white mesh file
-L | --CSF | --LCR <file name (read only): Mesh of VOID>
input pial mesh file
-g | --graph <string>
sulcus graph
-m | --model <string>
gyri model: Choice of the sulcus/sulcus relations
-l | --level <string>
level model: choice of the level of description file *.def
-i | --input <string>
input MRI volume (for dimensions)
-v | --volume <filename: carto_volume of FLOAT>
output thickness volume
-s | --sulciname <string>
Attribute for the name of the sulci in the graph (name or label)
[ -n | --numbercc | --nbcc <S64> ]
nb of connected components (default=5)
[ --de <FLOAT> ]
distance threshold (default=10 mm): max distance between the voxel and its
projection
[ --dp <FLOAT> ]
distance threshold (default=10 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)
siMeshSulciProjection
siMeshSulciProjection
---------------------
Project sulcus bottom points (voxels) on mesh texture (nodes). If <gyri model>
is specified, 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.
Options :
-i | --input <file name (read only): Mesh of VOID>
input mesh
-g | --graph <file name (read only): Graph>
input sulci graph
-o | --output <filename: texture of S16>
output sulci texture: projected sulci texture
[ -c | --curvature <file name (read only): texture of FLOAT> ]
input curvature texture
[ -m | --model <string> ]
input gyri model: Choice of the sulcus/sulcus relations
-l <string>
folds translation level model
-v | --volume <string>
input MRI volume (just to get dimensions)
-s | --sulciname <string>
sulci attribute for labels (name or label)
[ -K <FLOAT> ]
curvature coef: influence of the curvature. Default = 2
-t | --translation <string>
output translation file: correspondance label string->short_label, required
by siParcellation
[ -e | --demin <FLOAT> ]
euclidean distance threshold: max distance between a voxel and its
projection. Default = 5 mm
[ -p | --dpmin <FLOAT> ]
plane distance threshold. Default = 2 mm
[ -V | --Volume_radius <FLOAT> ]
closing volume radius: radius for the sulci closing in mm. Default = 1.5 mm
[ -M | --Mesh_radius <FLOAT> ]
closing radius for mesh. Default = 2.25
[ -a | --alpha <FLOAT> ]
estimation_ratio: distance threshold for detecting outliers for affine
projection estimation. Only points closer than (estimation_ratio * dmin)
are used for the estimation. Default = 1
[ --connectivity <boolean> ]
underlying mesh metric : mesh (default) or euclidean connexity
[ -n | --numbercc <S64> ]
number_connex_components: minimal number of point in each connected
component. Default = 4
[ -u <boolean> ]
project unknown 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)
siMkModelEdges
usage :
/casa/host/build/bin/siMkModelEdges [-o num] modelGraph.arg labelsFile adapFile.mod foldgraphlist
/casa/host/build/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 : /casa/host/build/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: carto_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): carto_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 :
/casa/host/build/bin/siRelax paramFile
/casa/host/build/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
--------------------
Compute parcellation in sulcal regions. The input sulci texture must be defined
by siMeshSulciProjection
Options :
-i | --input <file name (read only): Mesh of VOID>
grey/white mesh file
-o | --output <filename: texture of S16>
gyri texture: output timetexture file (sulci and gyri texture), 0: sulci,
1: sulcal regions
-g | --graph <filename: Graph>
output gyri graph
-s | --sulci <file name (read only): texture of S16>
input sulci texture (given by siMeshSulciProjection)
-m | --model <string>
gyri model: choice of the sulcus/sulcus relations ('gyri.gyr')
[ --3D <boolean> ]
compute 3D cortical ribbon gyrus graph
[ -b | --brain <file name (read only): Mesh of VOID> ]
brain mesh file (used if --3D is used)
[ -p | --parcelvol <filename: carto_volume of S16> ]
output gyri volume, used if --3D is used
[ -v | --valdomain | --value <S32> ]
grey value in input_grey_white vol (default = 100 )
[ -V | --volume | --Volume <file name (read only): carto_volume of S16> ]
input_grey_white: input grey/white volume, used if --3D is used
[ --sulcitraduction | --translation | --traduction <string> ]
correspondance label string->short_label required by siParcellation.
(default: sulcitraduction.txt
[ -T | --Time <U32> ]
input sulci texture timepoint (default = 0)
[ --connexity <boolean> ]
connexity or geodesic euclidean distance: use euclidean (default = 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)
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 : /casa/host/build/bin/siTriangModelmodel.arg folds.arg directory
siTryGauss
usage : /casa/host/build/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)
AimsFeaturesExtraction
AimsFeaturesExtraction
----------------------
Process an image using channels.
Each pixel is processed as a measure vectors.
Options :
[ -i <string> ]
Input image
[ -m <string> ]
Input mask file
[ -o <string> ]
Output image
[ -u <boolean> ]
Update minf file with extracted features info. [default : True]
[ -f <boolean> ]
Process features to output file. [default : True]
[ -c <string> ]
Image colors to extract (None, r, g, b, h, s, v, m (=Natural Gray)), e
(=Luminance Gray), x, y, z, L (L*), A (a*), B (b*)) [default : n (None)]
[ -n <boolean> ]
Extraction of neighbours' characteristics (in Gray images) [default :
False]
[ --nC <string> ]
Characteristics of the neighbours to extract (M : Mean, V : Variance, A :
Amplitude) [default : N (None)]
[ --nS <string> ]
Shape of the neighbourhood (D : Disk, C : circle, X : XCross, G :
GreekCross) [default : D]
[ --nA <S32> ]
Amplitude of the neighbourhood [default : 1]
[ --nL <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)
[ -t <boolean> ]
Texture information extraction [default : False]
[ --tC <string> ]
Texture feature to extract (L : LBP, H : Haralick, T : Tamura) [default : N
(None)]
[ --tLBP <string> ]
LBP parameters (W : without option, R : Rotation invariant, U : Uniformity
check) [default : N (None)]
[ --tA <vector of S32> ]
Amplitudes of the region
[ -p <string> ]
Parameters file path (text format). It contains information about the
number of features generated and the necessary border 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 | -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)
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 <FLOAT>
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
----------------------
Compute manual registration
Both arg files can be filled with anatomist roi module, but must:
- contain only one point per region
- regions must be correctly ordered: same roi_label or order of creation for
appariated points in both graphs
Options :
-f | --from <file name (read only): Graph>
from points
-t | --to <file name (read only): Graph>
to points
[ -o | --output <filename: AffineTransformation3d> ]
displacement file: default= <from>_TO_<to>.trm
[ --transfo <S32> ]
1=rigid, 2=simi, 3=affine (default=1)
[ -l | --loose <boolean> ]
registration with two points plus a point defining a plane
(inter-hemispheric plane)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
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)
bioDetectSlices
bioDetectSlices
---------------
Detect slices from multiple scan
Options :
-i <string>
Input original image
-n <S32>
Number of slices
[ -c <U8> ]
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]
[ -res <S32> ]
Scan resolution (in dpi)
[ -lt <S32> ]
Lower threshold [manual activation]
[ -ht <S32> ]
Higher threshold [manual activation]
[ -ms <FLOAT> ]
Minimal surface of slices [in mm2]
[ -dc <boolean> ]
Disable checks about surface and bounding boxes and automatic split of
slices [false]
[ -t <FLOAT> ]
Tolerance to slices surface variations [0.333333]
-o <string>
Output bounding boxes file (JSON)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <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 with the features previously computed.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
[ -l <vector of S32> ]
Output labels to use for the resulting segmentation
[ -c <vector of string> ]
Input 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 loaded with the features
previously computed.
Then, clusters are determined to approximate multi variate gaussian model.
(cf. bioVision algorithm)
Options :
-i <list of string>
Input features 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
[ -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)
AimsAdaptiveGaussianSmoothing
AimsAdaptiveGaussianSmoothing
-----------------------------
Calculate adaptive filtered image
filter each pixel according to adaptive sigma coming from sigma image
Options :
[ -col <string> ]
Input original color image to read
[ -gray <string> ]
Input grayscale image to read
-m <string>
Input mask image to read
[ -s <string> ]
Input masked sigma image to read
[ -sigma <FLOAT> ]
if there is no sigma image, apply unique sigma to all pixels
[default: '0']
[ -o <string> ]
Output filtered 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)
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 access / projection to image border
Options :
-i <file name (read only): volume of S16>
Input image (Binary, S16)
[ -o <string> ]
Output projection image [Default: extension *_proj added]
[ -od <string> ]
Output distance image [Default: extension *_dist added]
[ -bv <S16> ]
Background pixel value considered [Default=0]
[ -m <string> ]
Mask image S16 [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)
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 :
-par <file name (read only): VolumeRef of DOUBLE>
Input 2D parameters image
-map <filename: VolumeRef of DOUBLE>
Output generated feature map
[ -lab <file name (read only): VolumeRef 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
[ -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 52 features are saved in a parameters image
Options :
-col <file name (read only): VolumeRef of RGB>
Input original color image
-lab <file name (read only): VolumeRef of S32>
Input labelled image of the components
-vor <file name (read only): VolumeRef of S32>
Input voronoi image of the components
-par <filename: VolumeRef of DOUBLE>
Output 2D parameters image
X: component label
T: parameter
[ -mask <file name (read only): VolumeRef of S32> ]
Mask to use
[ -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]
[ -wt <boolean> ]
write text image
[default: true]
[ -ot <string> ]
Output parameters text
X: component label
T: parameter
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <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): VolumeRef of S32>
Input labelled image of the components
[ -vor <file name (read only): VolumeRef 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): VolumeRef of DOUBLE>
Input 2D parameters image
-vis <filename: VolumeRef 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)
AimsEdgeExtract
AimsEdgeExtract
---------------
Several methods
Options :
[ -i <string> ]
Input labelled image to read
[ -o <string> ]
Output edge 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)
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
-------------
? no doc...
Options :
-i | --input <string>
-o | --output <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)
AimsExtremaMap
AimsExtremaMap
--------------
Min-max cartography
Calculate extreme points in a circle or multiple circles with a predefined
radius
Options :
-i <string>
Input image to read
filtered grayscale image, background set to 0
-m <string>
Input mask to read
[ -o <string> ]
Output min-max cartography
[ -om <string> ]
Output min local image
[ -r <S32> ]
find extrema in a cricle or multiple circles
in the case of one circle, it's the radius
in the case of multiple circles, it's the maximal radius
[default: '1']
[ -mc <boolean> ]
find extreme points in multi-scale circle
[default: false]
[ -w <string> ]
weights of each circle, works when option mc is true
equal : w=1/nb_of_circle
nonequal : w=area_circle/area_all_circle
: extreme points in a larger circles is more confident
[default: 'equal']
[ -ml <boolean> ]
write seeds image
[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)
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
[ -b <string> ]
Background value to set if needed [default: value is estimated using border
of the input image]
-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 <FLOAT>
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)
AimsInterpolate
AimsInterpolate
---------------
Spline interpolation of a volume.
Only implemented for single channel data types for now.
Options :
--input | -i <string>
Input image.
[ --output | -o <string> ]
Output image.
[ --output-coefficients <string> ]
Output spline coefficients image.
[ --output-coefficients-old <string> ]
Output spline coefficients image with old resampler.
[ --reference | -r <string> ]
Reference image: its voxel size will be used.
It is overriden by "--vs" options.
[ --order <U32> ]
Interpolation order (default: 3).
[ --derivative <U32> ]
Derivative (default: 0).
[ --direction <vector of S32> ]
Derivative direction.
[ --type | -t <string> ]
Output data type: (default: same as input)
[ --scalar <boolean> ]
Get a scalar value in multi directional cases (der, der2...).
- In der 1 case: compute the norm
- In der 2 case: compute the determinant
(default: true if no direction given)
[ --precision <string> ]
- f[ast]: optimized spline equations. (very fast, default)
- r[ecursive]: runtime recursive evaluation (very slow, precise)
- t[abular]: precomputed splines values (fast, unprecise)
By default, a fast mode using precomputed spline values is used. By
enabling this option, exact spline computation is triggered.
Be aware that only the recursive and tabular mode work with any spline and
derivative order.
[ --dim-x | -dx <S64> ]
Output X dimension. (default: same as input)
[ --dim-y | -dy <S64> ]
Output Y dimension. (default: same as input)
[ --dim-z | -dz <S64> ]
Output Z dimension. (default: same as input)
[ --vs-x | -sx <FLOAT> ]
Output X voxel size. (default: same as input)
[ --vs-y | -sy <FLOAT> ]
Output Y voxel size. (default: same as input)
[ --vs-z | -sz <FLOAT> ]
Output Z voxel size. (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 | -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)
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
--------------------
Registration according to Mutual Information Method
Options :
-r | --reference <file name (read only): bucket of S16>
ref (bucket_SHORT file)
-t | --test <string>
source S16 test data (to register)
[ --Tx <FLOAT> ]
Tx, Ty, Tz: Init Translaction coord [default=0.0,0.0]
[ --Ty <FLOAT> ]
[ --Tz <FLOAT> ]
[ --dTx <FLOAT> ]
[ --dTy <FLOAT> ]
[ --dTz <FLOAT> ]
[ --Rx <FLOAT> ]
Rx, Ry, Rz: Init Rotation coord [default=0.0,0.0]
[ --Ry <FLOAT> ]
[ --Rz <FLOAT> ]
[ --dRx <FLOAT> ]
[ --dRy <FLOAT> ]
[ --dRz <FLOAT> ]
[ --interpolation <string> ]
interpolation method: 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(def) or pv
[ --gcinit <string> ]
Init with GravCenter: yes (def.) or no
[ --index <string> ]
index to be optimized: mi/cr [default=mi]
Mutual Information --> mi
Correlation Ratio --> cr
[ --serialnum <S32> ]
?
[ --pays_size <S32> ]
Half size the volume generated if algo=other activated
[ --graylevel <S32> ]
numb of classes in histogram pdf estimation [def.=64]
[ --masksize <S32> ]
size of the gaussian convolution mask in pdf estimationfor Mutual
Information [default=5]
[ --error <FLOAT> ]
tolerance on results [default=0.00001]
[ --seuiltest <FLOAT> ]
[0.1]
[ --seuilref <FLOAT> ]
[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)
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)
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)
AimsRegionGrowingExtrema
AimsRegionGrowingExtrema
------------------------
Individualize cells based on extrema map.
Extract cell centroids as seeds from extrema map (value ranges from 0 to 1) and
initiate a circle for each seed. Then process each point in the circle, make a
competitive region growing according to a contour-based model.
This model works on points, based on 3 information: normalized expansion
direction, curvature and expansion speed based on intensity of extrema map
Options :
[ -par <string> ]
Input parameters image to read
seeds imperatives
[ -col <string> ]
Input color image to read
[ -cc <string> ]
Input component connexe image to read
[ -mask <string> ]
Input mask image to read
[ -is <string> ]
Input seeds image to read
[ -ie <string> ]
Input extreme image to read
[ -iter <S32> ]
maximal iteration for region growing
[default: 50]
[ -th <FLOAT> ]
restrictive intensity for region growing
expanding rapid for small restrictive intensity and slow for big
restrictive intensity
[default: 0.7]
[ -dm <S32> ]
maximal distance bewteen two contour points
[default: 3]
[ -c <S32> ]
complementary coefficient for progression of contour
the bigger this coefficient is, the rapidder the expansion is.[default:
'4']
[ -wc <boolean> ]
write cells+seeds+contours image
[default: true]
[ -wp <boolean> ]
write label progression image
[default: false]
[ -oc <string> ]
Output cells+seeds+contours Image
[ -ol <string> ]
Output label Image
[ -op <string> ]
Output contour progression 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)
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)
AimsSigmaImageCalculate
AimsSigmaImageCalculate
-----------------------
Create sigma image
Options :
[ -col <string> ]
Input original color image to read
[ -cc <string> ]
Input label image to read
[ -po <string> ]
Input parameter image (original) to read
-c <string>
Input accumulated contour image to read
-fc <vector of string>
Input list of image contours+seeds
1 : contour, 2 : seed
-fl <vector of string>
Input list of image labels
-fp <vector of string>
Input list of image parameters
[ -sb <S32> ]
first sigma to process
[default: '1']
[ -fix <S32> ]
first sigma to process
[default: '1']
[ -o <string> ]
Output sigma 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)
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)
AimsSubSamplingConservative
AimsSubSamplingConservative
---------------------------
Map high resolution information to a lower resolution.
This process insures that no information is lost (in the sum case, both sums
over the whole volume should be equal) and that the millimetric coordinate
system is identical (no shift is introduced).
Options :
--input | -i <string>
Input volume.
[ --mask | -x <string> ]
Input mask. Must be of the same type as the input.
[ --reference | -r <string> ]
Input reference volume. Output voxel size and dimensions will be read from
it.
--output | -o <string>
Output low reolution volume.
[ --type | -t <string> ]
Output type (default: same as input)
[ --mode | -m <string> ]
Mapping mode:
s[um] (default), m[ean], v[ariance]
[ --voxel-size | -vs <vector of FLOAT> ]
Output voxel size (default if no reference: 1 1 1 * mm)
[ --dimension | -dim <vector of S32> ]
Output dimensions (default if no reference: based on 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 | -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)
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, ...)
[ -l <string> ]
Output minima 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 | -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)
bioCellBoundingBoxesGenerate
bioCellBoundingBoxesGenerate
----------------------------
Test procedure to define cell bounding box
Options :
-i <file name (read only): volume of U8>
Input image (U8)
[ -n <S32> ]
Minimum cell number to define [Default: 100 fov]
[ -r <FLOAT> ]
Minimum cell radius [Default: 3 µm]
[ -l <U8> ]
Value of the label to be processed [Default: v=1]
[ -f <FLOAT> ]
Ratio occupancy [Default: 50% = 0.5 of small cell]
[ -m <S32> ]
FOV size, multiple of cell size [Default: 2x cell radius]
[ -c <S32> ]
FOV centering, GC centered [Default: 2]
-o <filename: volume of U8>
Output image (U8)
[ -b <filename: object> ]
Output boundingbox (JSON)
[ -t <filename: volume of U8> ]
Output image temporary (squares tested / kept)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
bioCellEvaluate
bioCellEvaluate
---------------
*** Computation of connected components map ***
Options :
[ -i <string> ]
Input Graph to read
[ -m <string> ]
Input mask image to read
[ -l <string> ]
Input automated segmentation (label) image to read
[ -par <string> ]
Input automated segmentation (label) image to read
[ -s <string> ]
Input automated segmentation (seed) image to read
[ -o <string> ]
Write a txt file
[ -oc <string> ]
Write a txt file
[ -ol <string> ]
Write a txt 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)
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)
bioComponentConnexe
bioComponentConnexe
-------------------
*** Computation of connected components map ***
Options :
-i <string>
Input segmented image
[ -m <S64> ]
Mimimal component size to consider
[ -M <S64> ]
Maximal component size to consider
-o <string>
Output connected components image
[ -s <string> ]
Write stats in a file including label + 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)
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.
-if <string>
Input feature 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)
bioRenumberConnectComp
bioRenumberConnectComp
----------------------
Renumbering of touching labels produced in large datasets using HPC and
SomaWorkflow
Options :
-i <string>
Label input image
[ -m <string> ]
Label maxima input image
-o <string>
Correspondance table of labels
[ -c <string> ]
structuring element connectivity ( 4xy / 4xz / 4yz / 6 / 8xy / 8xz / 8yz /
18 / 26 / ... ) or shape ( cube / sphere / cross / ... ) [default: 8xy]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (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)
bioStatDominanceAppli
bioStatDominanceAppli
---------------------
Compute statistical dominance application to image
Options :
-i <string>
Input volume image
--radius <S32>
Radius size [Default: 20 pixels]
[ --threshold <FLOAT> ]
Intensity threshold [Default: value of 1/3 of maximum]
-o <string>
Output SDA volume 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)
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
[ --weightsFilename <string> ]
Weights text file matching bundle file input
-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
[ -weightsFilename <string> ]
Weights text file matching bundle file input
-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
[ -mt <string> ]
Mix type : label (majority) or level (default), used only in projection
mode (-op=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)
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 of a volume onto a surface bny interpolating surface vertices in the
volume
Options :
-im | --inMesh <string>
input Mesh
-iv | --inVol <string>
input Volume
-o | --outTex <string>
output Texture
-t | --type <S32>
interpolation type (default: 0=trilinear, 1=nearest neighbor
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <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
------------------------
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
...
Options :
-i | --input <string>
coordinates file
-m <file name (read only): Mesh of VOID>
atlas mesh
-u | --longitude <file name (read only): texture of FLOAT>
longitude texture
-v | --latitude <file name (read only): texture of FLOAT>
latitude texture
-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)
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)
DiscoFFDMetrics
DiscoFFDMetrics
---------------
Compute metrics on a displacement field representing a free-form deformation
(FFD)
Options :
--input | -i <file name (read only): VolumeRef of POINT3DF>
input displacement field
[ --divergence <filename: VolumeRef of FLOAT> ]
output: divergence of the coordinate field
[ --jacobian-det <filename: VolumeRef of FLOAT> ]
output: determinant of the Jacobian matrix of the coordinate 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)