f|*.nii.gz
Defined in file: brainvisa/types/builtin.py
01 Create Freesurfer subject from T1 anatomical image
01. DICE calculation (Batch mode) : FFD vs median subsample of volume
02. DICE calculation (Batch mode) : transformations evaluation
03. DICE calculation (batch mode) : DICE vs subsample of segmentation
04. DICE calculation (Batch mode) : FFD by different knot grids
05. DICE calculation (Batch mode) : FFD vs different combinations of color components on photo
06. DICE calculation (Batch mode) : FFD with different knot grid positions
1 - Mask from SPMt
2 - Primal Sketch from SPMt
2D Parcellation to 3D parcellation
2D to 3D
3D hierarchical analysis
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
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 clusters inspect tool
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 Connectivity Profiles of a Specific Cortical Element
Anatomist Show Connectivity Profiles of a Specific Cortical Element, Atlas pipeline variant
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 connectivity matrix
Anatomist view connectivity matrix, Atlas pipeline variant
Anatomist view reorder matrix from labeled texture
Anatomy Normalization (using AimsMIRegister)
Anatomy Normalization (using Baladin)
Anatomy Normalization (using FSL)
Anatomy Normalization (using FSL) with Re-initialization
Apply direct or inverse Transformation
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 Silhouette Width
AxialInterleavedVolumeExtraction
AxialSliceDeletion
AxialSliceListReplacement
AxialSliceReplacement
AxialSlicesPermutation
Baladin Normalization Pipeline
Baladin Normalization to AIMS converter
Basic Mixture Fitting
Bayesian Segmentation
Bias correction from B1 map
Block matching transformation estimation
Border generation
Brain Detection
Brain Detection (Utrecht)
Brain Mask Segmentation
Brain Normalisation and Masking
Brain Parcellation (EM)
Brain Volumes
BrainVISA Show Histo analysis
Bruker MRI : sequence preprocess
Calcul DICE's score on masks/labels volume
Calibration
CAT12 - Segment
Change Template Referential
Cingular Pole Projection
Classifier MLP
Classifier SVM
Classifier tests
ClearMap formats conversion
ClearMap resampling
Cluster detection
Clustering From Reduced Individual Matrix
Color combination generator
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 Grey / White / CSF / Skull / Scalp Mask
Compute GTM PVC based methods
compute intensity normalization
compute one tissue mask
Compute pairwise distances for a given sulcus
Compute T statistics and p-values
Compute voxel-wise between-group difference
Compute voxel-wise descriptive statsitics
Connected component extraction
Conversion of Freesurfer images to original t1mri space
Conversion of meshes to aims referential
Conversion of native (unresampled) meshes to aims referential
convert Dicoms to Nifti images
Convert Freesurfer images to nifti format
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 an Average Volume from a 4D-Volume
Create an Average Volume from Different Volumes
Create average template
Create Cortical Constraints Texture
Create DISCO deformation field from subjectA to subjectB
Create DISCO+DARTEL deformation field from subjectA to subjectB
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
DatScan resample SPECT natives
Delta permutation null-hypothesis
Delta permutation voxel-wise inference
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
Dicom to Nifti Converter Using Aims
Dicom to Nifti Converter Using MRICRON
Digital atlas prepare pipeline
DigitalAtlasRegistrationOnVolume
DigitalAtlasRegistrationOnVolumeParallel
Draw bounding boxes
Edit histo analysis
Elastix Registration
Elastix transformation estimation
Evaluation pipeline
Evaluation pipeline
Extract & Import T1 MRI ROI
Extract components using the morphological reconstruction
Extract connected components in order
FastMarching_AP_Segmentation 2D
FastMarching_AP_Segmentation 3D
Feature Extraction
Field of view processing
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 / BrainVisa full pipeline
FreeSurfer from MGZ Converter
FSL Normalization Pipeline
FSL Normalization to AIMS converter
FSL to AIMS transformation converter
Fusion Linear Contrasts
Gaussian smoothing
GeneralImport
GenerateBorder
GenerateMask
Get FreeSurfer Cerebellum in split mask
Get Hemi Surface
Get Spherical Brain Hull
Get Spherical Hemi Surface
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
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 slices extraction
Histology: 3D reconstruction pipeline
Histology: multiple 3D reconstruction pipeline
Import Baby T2 MRI
Import Brain Mask
Import Dicom T1 MRI
Import FLAIR MRI
Import FreeSurfer grey/white segmentation to Morphologist
Import FSL Connectomes.
Import MNI CIVET Segmentation
Import PET mean
Import SPMt for structural analysis
Import T1 MRI
Import T1 MRI, longitudinal version
Import T1MRI (nifti) about PET subject
Import volBrain results into a brainvisa database
ImportData
Individual clusters from atlas
IndividualizingAndStackingMultipleSlices
IndividualizingSlices
Inner Surface Initialization
Inner Surface Initialization (Utrecht)
Insular Pole Projection
Intensity normalisation PET Pipeline (spm12)
IntensityVolumeNormalization
InteractiveSubvolumeExtraction
Interhemispheric plane correction
Interlace multiple volumes
intersect ROI mask with grey/white mask Generic
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
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 volume generation
Median subsampling on volume
ml - Classify features image
ml - Features extraction using feature description file
ml - Parallel classification
ml - Parallel features extraction using feature description file
ml - PCA visualization
ml - Segmentation pipeline
Morphological operators application
Morphologist 2011
Morphologist 2012
Morphologist 2013
Morphologist 2015
Morphologist 2021
Morphomaths
Morphomaths basic
Move volume between MNI - T1MRI - PET (spm12)
MRI-PET registration
Multiple channel volume preprocessing
Mutual information transformation estimation
New Referential
NonLinearVolumeRegistration
Normalization pipeline
Normalize intensities of a T1 MRI
Nuclear Imaging quality check
Optimal PiB Reference Region
Outline generation
Parallel permutations
Pet long QC comparison SUV
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
PVC pipeline
QC rawdata PET
QC rawdata SPECT
QC recons SPECT
Quality control for Pet with MRI Pipeline
Quantification
Quantification: multiple 3D hierarchical analysis pipeline
RBV - sGTM
Read and complete AC-PC files
rectify internal image transformation from reference
Reduced Individual Matrix From Filtered Reduced Profile
Reference registration pipeline
Registration pipeline
Reorient Anatomy
Resample images into a Talairach-aligned grid
Resample ROI graph
Resample to Template Space
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 based analysis PET Pipeline (spm12)
ROI drawing
ROI quantification
ROISymetrizationAnd3DAnalysis
Segmentation of Cerebellum, Central Grey Nuclei and Ventricules (Utrecht)
Segmentation of Corpus Callosum
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
SPCN - 01 - Model estimation
SPCN - 02 - Model application
Split Brain Mask
Split Brain Mask
SPM - Brain Tissues Volumes
SPM : template generation pipeline
SPM : template registration pipeline
SPM Normalization Pipeline
SPM quantification
SPM to AIMS transformation converter
spm12 - Coregister: Estimate & Reslice - generic
spm12 - Coregister: Estimate Only
spm12 - DARTEL - Normalise to mni - generic
spm12 - Deformations : apply deformation field- generic
spm12 - Image calculator - generic
spm12 - Realign: Estimate & Reslice - generic
spm12 - Segment
spm12 - serial longitudinal registration
spm12 - serial longitudinal registration - generic
SPM12 - Slice Timing - generic
spm8 - Coregister: Estimate & Reslice - generic
spm8 - DARTEL - Normalise to mni - generic
spm8 - Deformations : apply deformation field- generic
spm8 - High-Dimensional Warping - generic
spm8 - Image calculator - generic
spm8 - New Segment
spm8 - Realign: Estimate & Reslice - generic
spm8 - VBM Segmentation - generic
Stacking
StackingIndividualSlices
StackingPhotographs
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 recognition with Deep CNN
Sulci Skeleton
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
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
uncompress any disk item
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
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
Vip Bias Correction
VIP Bias Correction
Vip Get Brain
Vip Histogram analysis
Vip Split Brain
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 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
anatomical Template
ANTs Elastic Transformation
Any Type
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
Bottom Volume
Bounding Box Points
BP ROI
Brain Mask
Brain Mask DISCO DARTEL
Cerebellum ROI
CGN ROI
Cingular Pole Template
Cingular Pole Template Subject
Connectivity Matrix
Corpus Callosum mask
Cortex Catchment Bassins
Cortex Skeleton
CSF+GREY Mask
CSFluid Probability Map
Curves graph
Diffusion Mask
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
GM Probability Map
Grey White Mask
Grey White Mid-Interface Volume
Gyri White Volume
Head Mask
Hemispheres Template
Histology scan
Hull Junction Volume
Intracranial labels
Intracranial mask
Jacobian determinant
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
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:Morpho Skull Stripping Mask
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
Parcellation volume
PET mean
PET mean smoothed
PET parametric
PET parametric smoothed
Phantom non-specific activity ROI
Probabilities Volume
Projection convolution kernels
Quantification ROI
quantitative analysis label volume
Rainbow 3D volume
Raw FLAIR MRI
Raw T1 MRI
Raw T1 MRI Brain Masked
RawFreesurferAnat
reference region mask
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 mask
ROI mask coregistered in CT space
ROI mask coregistered in NM space
Simple Surface Volume
Simulated MRI
SPECT native
SPECT quantification reference ROI
SPECT quantification ROI
SPECT template non-specific activity ROI
Split Brain Mask
SPM deformation field
SPMt map
Subcortical labels
Sulci Volume
Sulci Voronoi
T1 Brain Mask
T1 FreesurferAnat
T1 MRI
T1 MRI 4D Bias Normalized DISCO DARTEL
T1 MRI Bias Corrected
T1 MRI Bias Corrected Normalized
T1 MRI Bias field
T1 MRI Denoised
T1 MRI Denoised and Bias Corrected
T1 MRI Edges
T1 MRI Filtered For Histo
T1 MRI intracranial labels
T1 MRI Mean Curvature
T1 MRI mid-point average
T1 MRI tissue probability map
T1 MRI tissue probability mask
T1 MRI Variance
T1 MRI White Matter Ridges
T2 Brain Mask
T2 White matter Mask
Tissue probability map
Topo Brain
Tracking regions
Tracking regions graph
Ventricule ROI
WM Probability Map