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Defined in file : brainvisa/types/builtin.py

Used in the following processes

02 Launch Freesurfer full pipeline recon-all
03. DICE calculation (batch mode) : DICE vs subsample of segmentation
09 Converting labels to readable ascii format.
3D hierarchical analysis
3D-HAPi: 3D Histology Analysis Pipeline
[ANTs] Apply Transform
[ANTs] Registration (Linear + Elastic Simplified)
[Binary Volume] Extract Bounding Box (BinaryBoundingBox)
[Binary Volume] Extract Bounding Box from Binary (BoundingBoxCalculation)
[Parcellation] Generate segmentation scores
[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
Aggregate optimization cartography
Automatic bounding boxes detection
Average Subject Longitudinal Pipeline
AxialSliceListReplacement
Binary image: bounding box calculation
Block matching transformation estimation
Border generation
Bounding box transformation application
Brain Parcellation (EM)
Calibration
CAT12 - Segment - generic
Cingular Pole Texture From Freesurfer Label Texture
Clustering scores
color normalization GAN
Color segmentation: class selection
Color segmentation: feature based classification
Compute GTM PVC based methods
Connected component extraction
Constellation Individual Clusters from atlas pipeline - FSL connectome
Constellation Individual Pipeline - FSL connectome
convert Dicoms to Nifti images
Converting freesurfer labels to GIFTI textures.
Create database
CZI only: Automatic extract meta-data bounding boxes
Dendrogram
DICE calculation : DICE on label vs subsample of segmentation
Dices table (and graph) generator
Dicom to Nifti Converter Using Aims
Dicom to Nifti Converter Using MRICRON
DigitalAtlasRegistrationOnVolumeParallel
Download Allen Brain Atlas
Draw bounding boxes
Elastix Registration
Elastix transformation estimation
Export PDF Board from database
Extract Nifti Files from Brainvisa database
Extract sub list of images
Extract subvolume
Feature Extraction
Field of view processing
Free form deformation registration pipeline
Free form deformation transformation application
Free form deformation transformation estimation
FSL Connectome.
Generate optimization cartography workflow
Generate overlap cartography
Generate thumbnails
Global graph property
Group creation/modification (from many groups, covariate or image list)
Group subjects by type
Heat map generation
Histological scan spatial reorganization
Histological slices extraction
Histology : 3d reconstruction pipeline
Histology: 3D reconstruction pipeline
Histology: multiple 3D reconstruction pipeline
Import DatScan Multiple
Import Dicom T1 MRI
Import MRI Nii of Many Subjects
Import new assessment (dicom)
Import Reference dicom
Individual Longitudinal Pipeline
Individualize labeled volume
InterVolumesSliceCoregistration
Jaszczak - FWHM Determination based on RC
Linear registration pipeline
Manual: Edit bounding box
Manual: Extract bounding boxes
Mask application
Mask generation
Mask processing
mean pets
Merge bounding box files
ml - Parallel multiple images features extraction
ml - Weighted Random Forest image-level cross-validation pipeline
Morphometry statistics
Multiple registration pipeline
Mutual information transformation estimation
Parallel delta permutations
Parallel permutations
patch assembling
patch generation
Photography: 3D reconstruction pipeline
Quantification: multiple 3D hierarchical analysis pipeline
Realign PET (spm 12)
Realign PET (using SPM)
Reference registration pipeline
Registration pipeline
Remove tag in dicoms
Rename Dicoms for multiple subjects
RenameImageSeries
Replace char in paths
Resampling
Select folds & relations with good recognition percentage
Smoothing filter
SPAM models installation
SPCN - 01 - Model estimation
Split ROI
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 - Deformations : apply deformation field- generic
Stacking
Study definition manager
Sub sampling
Subcortical From Freesurfer To MarsAtlas Parcellation
Sulci graph morphometry inter subject
Sulci SPAM
T-test
training GAN
volume - unstack slices (GIS only)
Write the connectome of a given parcellation

Associated formats

Directory

Associated ontology rules

Key attributes

  • PetPhantom :
  • phantom ,  center ,  acquisition ,  reconstruction
  • brainvisa-3.2.0 :
  • Study ,  center ,  subject ,  acquisition ,  tracer ,  reconstruction ,  rescan ,  acquisition_date ,  time_point ,  time_duration ,  analysis ,  graph_version ,  sulci_recognition_session ,  side ,  Template ,  from ,  processing ,  template ,  factorial_design ,  group_name ,  first_group ,  second_group ,  PVC_method ,  segmentation_method ,  factoriel_design ,  ROIReference ,  fwhm ,  nuisance_covariate_list ,  interest_covariate_list ,  pet_intersection ,  reconDiam ,  manually_labelled ,  automatically_labelled
  • brainvisa-3.0 :
  • analysis ,  template ,  protocol ,  subject ,  category ,  acquisition
  • brainvisa-3.1.0 :
  • center ,  subject ,  acquisition ,  tracer ,  reconstruction ,  analysis ,  contrast ,  protocol ,  graph_version ,  sulci_recognition_session ,  side ,  from ,  template
  • medNuc_network :
  • modality ,  manufacturer ,  device_model ,  center_device_id