T1 Brain Mask

Return to index

Inheritance graph

Defined in file : brainvisa/toolboxes/morphologist/types/anatomy.py

Used in the following processes

Ana Brain Mask from T1 MRI
Ana Get Opened Whole Brain Surface
Ana Split Brain from Brain Mask
Brain Mask Segmentation
Compute Brain Mask
Correction Brain Mask from T1 MRI
Correction Split Brain from Brain Mask
Import Brain Mask
Import FreeSurfer grey/white segmentation to Morphologist
Import MNI CIVET Segmentation
Segmentation of Corpus Callosum
Simplified Morphologist 2025
Split Brain Mask
Split Brain Mask
Validation Pipeline
Validation_3 Brain Mask from T1 MRI
Vip Get Brain
Vip Split Brain

Associated formats

Aperio svs
BrainVISA volume formats
DICOM image
Directory
ECAT i image
ECAT v image
FDF image
FreesurferMGH
FreesurferMGZ
GIS image
gz compressed MINC image
gz compressed NIFTI-1 image
Hamamatsu ndpi
Hamamatsu vms
Hamamatsu vmu
JPEG image
Leica scn
MINC image
NIFTI-1 image
Sakura svslide
SPM image
TIFF image
TIFF(.tif) image
Ventana bif
Zeiss czi

Associated ontology rules

  • brainvisa-3.0 :
    • {protocol}/{subject}/segment/brain_<subject>
    {protocol}/{subject}/segment/brain_<subject>_*
    {protocol}/{subject}/segment/{acquisition}/brain_<subject>
    {protocol}/{subject}/segment/{acquisition}/brain_<subject>_*
  • brainvisa-3.1.0 :
    • {protocol}/{subject}/t1mri/{acquisition}/{analysis}/segmentation/brain_<subject>
  • brainvisa-3.2.0 :
    • {center}/{subject}/t1mri/{acquisition}/{analysis}/segmentation/brain_<subject>
    {center}/{subject}/longitudinal_preprocessings/spm12Serial/avg_{acquisition_sequence}/{analysis}/<subject>_{acquisition}_to_avg_<acquisition_sequence>_brain_mask
    {center}/{subject}/longitudinal_preprocessings/spm12Pairwise/avg_{acquisition_sequence}/{analysis}/<subject>_{acquisition}_to_avg_<acquisition_sequence>_brain_mask
  • morphologist-bids-1.0 :
    • sub-{subject}/ses-{session}/anat/t1mri/{acquisition}/{analysis}/segmentation/brain_<subject>
  • morphologist-bids-2.0 :
    • sub-{subject}/ses-{session}/{bids}/ana-{analysis}/segmentation/sub-<subject>_ses-<session>_<bids>_brain

    Key attributes

  • brainvisa-3.0 :
    • protocol ,  subject ,  filename_variable ,  acquisition
  • brainvisa-3.1.0 :
    • protocol ,  subject ,  acquisition ,  analysis
  • brainvisa-3.2.0 :
    • rescan ,  time_duration ,  time_point ,  acquisition_date ,  center ,  subject ,  acquisition ,  analysis ,  acquisition_sequence ,  processing
  • morphologist-bids-1.0 :
    • rescan ,  time_duration ,  time_point ,  acquisition_date ,  subject ,  session ,  acquisition ,  analysis
  • morphologist-bids-2.0 :
    • rescan ,  time_duration ,  time_point ,  acquisition_date ,  subject ,  session ,  bids ,  analysis