d|*
Defined in file: python/brainvisa/processes.py
00a. Talairach transform extraction
01. DICE calculation (Batch mode) : FFD vs median subsample of volume
01. Prepare grey and white maps for DARTEL
01. Sulcal imprints extraction
01. Sulci Label Translation
02 Launch Freesurfer full pipeline recon-all
02. DARTEL Template Creation
02. DICE calculation (Batch mode) : transformations evaluation
02. Template building
02a. Sulci To Be Removed
02b. Sulci To Be Added
03. DARTEL Images Warping
03. DICE calculation (batch mode) : DICE vs subsample of segmentation
03. Grid deformation
03. Sulci Merging
04. DARTEL Images Inverse Warping
04. DICE calculation (Batch mode) : FFD by different knot grids
04. Sulci Not to Be Pruned
04. Volume deformation
05. DICE calculation (Batch mode) : FFD vs different combinations of color components on photo
05. Sulci Weight
06. DICE calculation (Batch mode) : FFD with different knot grid positions
09 Converting labels to readable ascii format.
1 - Mask from SPMt
2 - Primal Sketch from SPMt
2D Parcellation to 3D parcellation
2D to 3D
3D hierarchical analysis
3D-HAPi: 3D Histology Analysis Pipeline
3DFFDTransformationApplication
3DFFDTransformationEstimation
5 - Compute Grey white Interface Mesh
[ANTs] Apply Transform
[ANTs] Registration (Linear + Elastic Simplified)
[Atlas] Convert Volume of Labels / ROI graph
[Atlas] Hierarchy Tools
[Binary Volume] Extract Bounding Box (BinaryBoundingBox)
[Binary Volume] Extract Bounding Box from Binary (BoundingBoxCalculation)
[Parcellation] Generate segmentation scores
[Proba Volume] Convert to colored atlas for visualization
[Reference Segmentation] Convert and merge
[Volume of Labels] Compute Clique Statistics
[Volume] - Split parallel
[Volume] Block Matching
[Volume] Connected Component
[Volume] Connected Components
[Volume] Convert
[Volume] Flip
[Volume] Flip
[Volume] Gray level to time series
[Volume] Inter Slice Normalize
[Volume] Linear Combination
[Volume] Linear Combination
[Volume] Mask
[Volume] Mask
[Volume] Morphological Closing
[Volume] Morphological Opening
[Volume] Replace Level
[Volume] Replace Level
[Volume] Resample
[Volume] Segment brain from photo (mac)
[Volume] Smoothing
[Volume] Smoothing
[Volume] SubSampling
[Volume] SubSampling
[Volume] SubVolume
[Volume] Threshold
[Volume] Threshold
AC/PC Or Normalization
Adaptive bandwidth generation
Adaptive gaussian filtering
Adaptive heatmap generation
Add Border To Image
Add gaussian noise in image background
AddScannerBasedReferential
Aggregate optimization cartography
Aims Converter
Align and Resample
Ana Brain Mask from T1 MRI
Ana Compute Hemi Grey White Classification
Ana Get Opened Hemi Surface
Ana Get Spherical Cortical Surface
Ana Split Brain from Brain Mask
Anat To FreeSurfer Meshes Transformation
Anatomist Fusion 3D/mesh
Anatomist Show 3D Activations
Anatomist Show 3D Fusion
Anatomist Show Bias Correction
Anatomist Show Brain Mask on T1 MRI
Anatomist show Commissure coordinates
Anatomist Show DISCO results in a common referential
Anatomist Show Elevation Map
anatomist Show fMRI-MRI Fusion
Anatomist Show Fold Graph
Anatomist Show Graph
Anatomist Show Grey White on T1 MRI
Anatomist Show GreyWhite Snake on T1 MRI
Anatomist Show Hemisphere With MRI
Anatomist Show Nucleus Graph
Anatomist Show Rainbow Volume
Anatomist Show Registration
Anatomist Show ROI
Anatomist Show Split Brain on T1 MRI
Anatomist Show Volume
Anatomist Show White Matter With MRI
Anatomist Show White Ridge on T1 MRI
Anatomist view reorder matrix from labeled texture
Anatomy Normalization (using AimsMIRegister)
Apply FFD on atlas label
Apply mask
Apply Transformation
ApplyFastMarching
ApplyPreprocessedTransformations
Atlas label extraction
Atlas Registration: Affine (MI/Newton)
Atlas Registration: Application
Atlas Registration: Non Linear (MI/FFD)
Atlas Registration: Select Evaluation Points
Automatic bounding boxes detection
Average cortical ribbon
Average Subject Longitudinal Pipeline
AxialInterleavedVolumeExtraction
AxialSliceDeletion
AxialSliceListReplacement
AxialSliceReplacement
AxialSlicesPermutation
B01. Bundles Label Translation
B02. Bundles To Be Removed
B03. Bundles Merging
B04. Bundles Not to Be Pruned
B05. Bundles Weight
Baladin Normalization Pipeline
Baladin Normalization to AIMS converter
Basic Mixture Fitting
Bayesian Segmentation
Bias correction from B1 map
Binary image: bounding box calculation
Block matching transformation estimation
Border generation
Bounding box transformation application
Brain Detection
Brain Detection (Utrecht)
Brain Mask Segmentation
Brain Normalisation and Masking
Brain Parcellation (EM)
Brain Tracts Filtering
Brain Volumes
BrainVISA Show Histo analysis
Bruker MRI : sequence preprocess
Calcul DICE's score on masks/labels volume
Calibration
CAT12 - Segment - generic
Change Template Referential
Cingular Pole Projection
Cingular Pole Texture From Freesurfer Label Texture
Classifier MLP
Classifier SVM
Classifier tests
ClearMap formats conversion
ClearMap resampling
Cluster detection
Clustering scores
Color combination generator
color normalization GAN
Color segmentation: class selection
Color segmentation: feature based classification
Color segmentation: model visualization
Compute and Split Brain Mask
Compute Average brain
Compute Average cortical ribbon
Compute Brain Mask
Compute Cortex image
Compute Cortical Fold Graph Upgrade From Old
Compute GTM PVC based methods
Compute pairwise distances for a given sulcus
Compute Pairwise mean distances
Compute T statistics and p-values
Compute voxel-wise between-group difference
Compute voxel-wise descriptive statsitics
Connected component extraction
Conversion of meshes to aims referential
Conversion of native (unresampled) meshes to aims referential
convert Dicoms to Nifti images
Converting freesurfer labels to GIFTI textures.
Copy data between databases
Copy Referential
Correction Brain Mask from T1 MRI
CorrectShiftStack
Cortex Topological Correction
Cortical Fold Arg (3.0)
Cortical Fold Graph (3.1+)
Cortical Fold Graph (general)
Cortical Fold Graph (one hemisphere)
Cortical Fold Graph 2007-2011 (general)
Cortical Fold Graph Upgrade Structure
Cortical Folds Graph
Create 4D volume from 3D volumes
Create a new DISCO Study from existing parameters
Create an Average Volume from a 4D-Volume
Create an Average Volume from Different Volumes
Create average template
Create Cortical Constraints Texture
Create database
Create DISCO deformation field from subjectA to subjectB
Create DISCO+DARTEL deformation field from subjectA to subjectB
Create DISCO+DARTEL deformation field toward the common space
Create FreeSurfer Meshes referential
Create histo analysis manually
Create Left Hemisphere Cortical Constraints Texture
Create points ROI
Create Right Hemisphere Cortical Constraints Texture
Create Sulcus Label Volume
Create Surface-Based Functional Data (Projection of fMRI Data onto the Cortical Surface)
Crop volume
CSF Classif
CTTimeSeriesFfdRegistration
CTTimeSeriesPreprocessing
CTTimeSeriesReconstruction
CTTimeSeriesRegistration
CZI only: Automatic extract meta-data bounding boxes
Dartel pipeline
DatScan resample SPECT natives
Deformation DISCO Pipeline
Deformation DISCO+DARTEL Pipeline
Delta permutation null-hypothesis
Delta permutation voxel-wise inference
Dendrogram
DICE calculation : DICE on label vs subsample of segmentation
DICE calculation : FFD on label with different knot grid
DICE calculation : FFD on label with different knot grid positions
DICE calculation : FFD vs different combinations of color components on photo
DICE calculation : transformations evaluation
DICE calculation: FFD vs median subsample of volume
DICE index
Dices table (and graph) generator
Dicom to Nifti Converter Using Aims
Dicom to Nifti Converter Using MRICRON
Digital atlas prepare pipeline
DigitalAtlasRegistrationOnVolume
DigitalAtlasRegistrationOnVolumeParallel
Disco and Dartel complete pipeline
Disco pipeline
Download Allen Brain Atlas
Draw bounding boxes
Edit histo analysis
Elastix Registration
Elastix transformation estimation
Evaluation pipeline
Evaluation pipeline
EXPERIMENTAL: Compute template descaling transformation
Experimental: Transform multiple volumes into the common space
Export PDF Board from database
Extract & Import T1 MRI ROI
Extract components using the morphological reconstruction
Extract connected components in order
Extract Nifti Files from Brainvisa database
Extract sub list of images
Extract subvolume
FastMarching_AP_Segmentation 2D
FastMarching_AP_Segmentation 3D
Feature Extraction
Field of view processing
Final deformation applied on graph
Final deformation applied on mesh
Final deformation applied on volume
Final deformation applied on voronoi and cortical ribbon
Fix normalized image referential
Flat-map image from rectangular mesh
FlipApplication
FlipApplicationOnASlice
Folds graph over-segmentation
FOV enlarge
Free form deformation registration pipeline
Free form deformation transformation application
Free form deformation transformation estimation
Freesurfer aparcstats2table
Freesurfer asegstats2table
FSL Connectome.
FSL Normalization Pipeline
FSL Normalization to AIMS converter
FSL to AIMS transformation converter
Fusion Linear Contrasts
Gaussian smoothing
GeneralImport
Generate optimization cartography workflow
Generate overlap cartography
Generate thumbnails
GenerateBorder
GenerateMask
Get FreeSurfer Cerebellum in split mask
Get Hemi Surface
Get Spherical Brain Hull
Get Spherical Hemi Surface
Global graph property
Gradient generation
Graph Point cloud Label
Graph Structure (3.0)
Graph Structure (3.1)
Graph To Volume Converter
Grey level replacement
Grey White Classification
Grey White Classification 2012
Grey white Interface
Grey White Surface 2012
GreyLevelConversionToActivity
Grid generation
Group subjects by type
Gyral Parcellation
Head Mesh
Heat map generation
Hemi Surfaces and Sulci Extraction
Hemisphere Cortical Folds Graph
Hemisphere Grey White Classification
Hemisphere Grey White Mesh
Hemisphere Grey White Topological Correction
Hemisphere Pial Mesh
Hemisphere Sulci Skeleton
Hemisphere Sulci Thickness and Volumes
Hemisphere Sulci Voronoi
Histogram Analysis
Histogram analysis
Histogram analysis
Histogram Analysis (for Morphologist)
Histological scan spatial reorganization
Histological slices extraction
Histology : 3d reconstruction pipeline
Histology: 3D reconstruction pipeline
Histology: multiple 3D reconstruction pipeline
Import Baby T2 MRI
Import Brain Mask
Import DatScan Multiple
Import Dicom T1 MRI
Import FLAIR MRI
Import FreeSurfer grey/white segmentation to Morphologist
Import FSL Connectomes.
Import MNI CIVET Segmentation
Import MRI Nii of Many Subjects
Import new assessment (dicom)
Import PET mean
Import Reference dicom
Import SPMt for structural analysis
Import T1 MRI
Import T1 MRI, longitudinal version
Import volBrain results into a brainvisa database
ImportData
Individual Longitudinal Pipeline
Individualize labeled volume
IndividualizingAndStackingMultipleSlices
IndividualizingSlices
Inner Surface Initialization
Inner Surface Initialization (Utrecht)
Insular Pole Projection
IntensityVolumeNormalization
InteractiveSubvolumeExtraction
Interhemispheric plane correction
Interlace multiple volumes
InterVolumesSliceCoregistration
IntraVolumePropagativeSliceRegistration
Invert
Label volume editor
Labeled volume: calculate the bounding box for each label
Leave-one-out RSS
Left Cingular Pole Projection
Linear Combination
Linear registration pipeline
Localize Talairach Coordinate
Manage group for longitudinal analysis
Manual Drawing of Cerebellum and Segmentation of Central Grey Nuclei from 2 Orthogonal Slices
Manual: Edit bounding box
Manual: Extract bounding boxes
Mask application
Mask generation
Mask processing
mean pets
Mean volume generation
Median subsampling on volume
Merge bounding box files
Mesh deformation component
ml - Classify features image
ml - Features extraction using feature description file
ml - Parallel classification
ml - Parallel features extraction using feature description file
ml - Parallel multiple images features extraction
ml - PCA visualization
ml - Segmentation pipeline
ml - Weighted Random Forest image-level cross-validation pipeline
Morphological operators application
Morphologist 2011
Morphologist 2012
Morphologist 2013
Morphologist 2015
Morphologist 2021
Morphomaths
Morphomaths basic
Morphometry statistics
MRI-PET registration
Multiple channel volume preprocessing
Multiple registration pipeline
Mutual information transformation estimation
New Referential
NonLinearVolumeRegistration
Normalization pipeline
Normalize intensities of a collection of T1 MRIs
Normalize intensities of a T1 MRI
Nuclear Imaging quality check
Outline generation
Parallel delta permutations
Parallel permutations
patch assembling
patch generation
PETScanAtlasAnalysis
PhotographicVolumePreprocessing
Photography: 3D reconstruction pipeline
Pial Mesh
Pipeline Baby
Pipeline Baby (Utrecht)
PixelSizeCalibration
Prepare For Morphologist
Prepare MRI
Prepare Subject for Anatomical Pipeline
Preprocessing and Atlas Registration
Primatologist
Projection using Convolution Kernels
QC table of a DARTEL Template
QC table of a DISCO Study
Quantification
Quantification: multiple 3D hierarchical analysis pipeline
Read and complete AC-PC files
Reference registration pipeline
Registration pipeline
Remove tag in dicoms
Rename Dicoms for multiple subjects
RenameImageSeries
Reorient Anatomy
Resample images into a Talairach-aligned grid
Resample ROI graph
Resample to Template Space
Resampling
Resampling
Resampling to image space
Resampling volume
Reset internal image transformation
RGB_roi_fill
RGBIntensityNormalization
RGBVolumeCreation
Right Cingular Pole Projection
Right Insular Pole Projection
Rigid registration with mutual information
ROI drawing
ROI quantification
ROISymetrizationAnd3DAnalysis
Segmentation of Cerebellum, Central Grey Nuclei and Ventricules (Utrecht)
Segmentation of Corpus Callosum
Select folds & relations with good recognition percentage
Simple ROI Editor
Simplified Brain Detection (Utrecht)
Simplified Morphologist 2015
Single delta permutation
Single file to volume series
Single permutation
Skull-Strip MRI
Skull-stripped brain normalization
Skull-stripping
Smoothing filter
SPAM models installation
SPAM recognition, local registration
SPCN - 01 - Model estimation
SPCN - 02 - Model application
Split Brain Mask
Split Brain Mask
Split ROI
SPM - Brain Tissues Volumes
SPM : template generation pipeline
SPM : template registration pipeline
SPM Normalization Pipeline
SPM quantification
SPM to AIMS transformation converter
spm12 - create warped
spm12 - Deformations : apply deformation field- generic
spm12 - Model Review - generic
spm12 - One sample T-test - generic
spm12 - Paired T-test - generic
spm12 - Results report
spm12 - Two sample T-test - generic
spm8 - create warped
spm8 - Deformations : apply deformation field- generic
spm8 - One sample T-test - generic
spm8 - Paired T-test - generic
spm8 - Two sample T-test - generic
Stacking
StackingIndividualSlices
StackingPhotographs
Study definition manager
Sub sampling
Subcortical From Freesurfer To MarsAtlas Parcellation
Subsampling
SubvolumeStacking
Sulcal Lines Extraction
Sulcal Lines Extraction Left
Sulcal Lines Extraction Right
Sulcal Lines Extraction With Options
Sulci Distance to Lesion
Sulci graph morphometry inter subject
Sulci recognition with Deep CNN
Sulci Skeleton
Sulci SPAM
Sulci Thickness and Volumes
Sulci Voronoi
Sulci Voronoi
Sulcus Parameterization
Sulcus Parameterization 2015
Surface Deformation
Surface Deformation (Utrecht)
Surfaces and Sulci Extraction
Surfacic Sulci To Labels Volume
Swap Bias Corrected MRI and Simulated MRI
T-test
T1 Bias Correction
T1 Bias Correction
T1 mapping maps: build using VFA method
T1 Pipeline 2007
Talairach Transformation
Talairach transformation from manual AC/PC
Talairach Transformation From Normalization
Test Classifier
Test Classifier 3
Threshold
Threshold and Normalize
Train classifier
Train MLP
Train SVM
training GAN
Transform a commissures AC-PC coordinates
Transform fibre bundles between subjects
Transform fibre bundles into the common space
Transform graph between subjects
Transform graph into the common space
Transform mesh between subjects
Transform mesh into the common space
Transform volume between subjects
Transform volume into the common space
UnstackingVolumeInIndividualSlices
Validation Pipeline
Validation_0 Commissure Coordinates
Validation_1 Bias Correction from T1 MRI
Validation_2 Nobias Histo analysis
Validation_3 Brain Mask from T1 MRI
Validation_4 Split Brain from Brain Mask
Validity Indexes
Varian MRI : sequence preprocess
Verify accuracy of inverse deformations
View Deformation Field as a displacement grid
View displacement arrows on a mesh
view images in a titled grid
View in hippocampic referential
View Jacobian Determinant of Deformation Field
View Sulci of all subjects before and after DISCO
Vip Bias Correction
VIP Bias Correction
Vip Get Brain
Vip Histogram analysis
Vip Split Brain
volume - unstack slices (GIS only)
Volume series to single file
Volume To ROI Graph Converter
VolumeResizing
Volumic Average
Volumic Deviation
Volumic Sulcus SPAM
Volumic T Test
White Matter Mesh
White Mesh Depth Map
White Mesh without decimation
Write a different measures in csv file
Write connectivity matrix as CSV File
Write the connectome of a given parcellation
Write Volume with MNI transformation in header
{Importer} Histology scan
{Importer} MRI
{Viewer} Affine Registration
{Viewer} Atlas Raw Labels
{Viewer} Atlas Raw Lateralization
{Viewer} Atlas Raw Prior
{Viewer} Bias Corrected MRI
{Viewer} Brain Mask
{Viewer} Cortex Roots
{Viewer} Cortex Skeleton
{Viewer} Evaluation Points
{Viewer} FFD Registration
{Viewer} Grey White Mask
{Viewer} Mid Interface
{Viewer} Mixture
{Viewer} Parcellation
{Viewer} Probabilities
{Viewer} Registered Atlas Labels
{Viewer} Registered Atlas Lateralization
{Viewer} Registered Atlas Template
{Viewer} Skull Stripping Mask
{Viewer} Split Brain Mask
{Viewer} Sulci Voronoi
{Viewer} Topology
2D Image
3D Volume
4D Volume
Acquisition
Analysis Dir
anatomical Template
Any Type
Atlas Results Dir
Average cortical ribbon DISCO DARTEL
Average T1 MRI Bias Brain Alone DISCO DARTEL
Average T1 MRI Bias DISCO DARTEL
Baby Automatic Grey White Mask
Baby Grey White Mask
Baby Manual White Mask
Baby White Ridges
Biology Directory
Blockface modality
Bottom Volume
Bounding Box Points
BP ROI
Brain Mask
Brain Mask DISCO DARTEL
Bvsession
Center
Cerebellum ROI
CGN ROI
Chi Square folder
Cingular Pole Template
Cingular Pole Template Subject
Coefficients GTM based PVC Directory
Connectivity Matrix
contrast
Corpus Callosum mask
Cortex Catchment Bassins
Cortex Skeleton
CSF+GREY Mask
CSFluid Probability Map
Curves graph
DARTEL analysis directory
DARTEL Results Dir
DARTEL Template Dir
Diffusion Mask
Directory
DISCO Study Dir
Elevation map
Error mask
FFD Displacement Field
fMRI
fMRI activations
Freesurfer aseg
Freesurfer Brain Mask
Freesurfer Cortical Parcellation
FreesurferAnat
Functional mask
Fus Det
Fus Det WM
FWHM PVC Directory
GM Probability Map
Grey White Mask
Grey White Mid-Interface Volume
Gyri White Volume
Head Mask
Hemispheres Template
Histology marker
Histology scan
Histology segmentations
Histology slices
Histology stacks
Hull Junction Volume
Label volume
Left Cingular Pole Template Subject
Left Cortex Catchment Bassins
Left Cortex Skeleton
Left CSF Mask
Left CSF+GREY Mask
Left Grey White Mask
Left Gyri Volume
Lesion distance map
Lesion Mask
Morphologist Grey White Mask
Native space ROI
Non-specific activity ROI
Nu FreesurferAnat
OLD CT directory
OLD PET directory
P:Atlas Clique Matrix
P:Atlas Raw Labels
P:Atlas Raw Lateralization
P:Atlas Raw Prior
P:Atlas Raw Template
P:Atlas Registered Labels
P:Atlas Registered Lateralization
P:Atlas Registered Prior
P:Atlas Registered Skull Stripping Mask
P:Atlas Registered Template
P:EM Parcellation
P:EM Parcellation Proba
P:EM Prior Proba
P:Inverted MRI Bias Corrected
P:Inverted MRI Mean Curvature
P:Modality
P:Morpho Skull Stripping Mask
P:MRI Analysis Directory
P:MRI Bias Corrected
P:MRI Bias Field
P:MRI Edges
P:MRI EM Bias Corrected
P:MRI EM Bias Field
P:MRI Filtered For Histo
P:MRI Mean Curvature
P:MRI Raw
P:MRI Variance
P:MRI VIP Bias Corrected
P:MRI VIP Bias Field
P:MRI White Matter Ridges
P:Parcellation
P:Reference Parcellation
P:Reference Parcellation Mask
P:Registration Target
P:Skull Stripping Mask
P:T1 MRI Analysis Directory
P:T2 MRI Analysis Directory
Parcellation volume
PET dynamic
PET dynamic realigned
PetSubject Contrast Dir
PetSubject PET Dyn
PetSubject PET Dyn NearMNI
PetSubject PET Dyn Realigned
PetSubject PET Dynamic
PetSubject PET Group Dir
PetSubject T1 Group Dir
Phantom non-specific activity ROI
Phantom PET dynamic
Phantom PET dynamic realigned
Phantom ROI PVC
Photo Registrations Directory
Photo Segmentations Directory
Photo Stacks Directory
Photos Directory
Postmortem modality
Probabilities Volume
Projection convolution kernels
Protocol
PVC Directory
Quantification ROI
Rainbow 3D volume
Raw FLAIR MRI
Raw T1 MRI
Raw T1 MRI Brain Masked
RawFreesurferAnat
Reference Dicom directory
Registration Directory
Ribbon Freesurfer
Right Cingular Pole Template Subject
Right Cortex Catchment Bassins
Right Cortex Skeleton
Right CSF Mask
Right CSF+GREY Mask
Right Grey White Mask
Right Gyri Volume
ROI
ROI analysis
ROI mask
ROI mask coregistered in CT space
ROI mask coregistered in NM space
RSF PVC Directory
Scans Directory
Session
Simple Surface Volume
Simulated MRI
Snapshots Dir
SPECT quantification reference ROI
SPECT quantification ROI
SPECT ROI analysis
SPECT SPM voxel-based analysis
SPECT template non-specific activity ROI
Spheres Folders for FWHM estimation
Split Brain Mask
Splitted Biological volume
SPM analysis
SPM group analysis
SPM voxel-based analysis
SPM workspace directory
SPMt map
Study Directory
Subject
Subjects Directory
Sulci Local SPAM transformations Directory
Sulci Volume
Sulci Voronoi
T1 Brain Mask
T1 FreesurferAnat
T1 MRI
T1 MRI 4D Bias Normalized DISCO DARTEL
T1 MRI Analysis Directory
T1 MRI Bias Corrected
T1 MRI Bias Corrected Normalized
T1 MRI Bias field
T1 MRI Edges
T1 MRI Filtered For Histo
T1 MRI Mean Curvature
T1 MRI Variance
T1 MRI White Matter Ridges
T2 Brain Mask
T2 White matter Mask
Tables Directory
Topo Brain
Tracking regions
Tracking regions graph
Ventricule ROI
Voxel by voxel comparison SPM workspace directory
WM Probability Map