Brain Mask

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Inheritance graph

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

Used in the following processes

Anatomist Show Brain Mask on T1 MRI
Compute and Split Brain Mask
Prepare For Morphologist
Skull-stripped brain normalization
Skull-stripping
Surfaces and Sulci Extraction
{Viewer} Brain Mask

Associated formats

Aperio svs
BrainVISA volume formats
DICOM image
Directory
ECAT i image
ECAT v image
FDF image
FreesurferMGH
FreesurferMGZ
GIS image
gz compressed ECAT i image
gz compressed ECAT v image
gz compressed GIS image
gz compressed MINC image
gz compressed NIFTI-1 image
gz compressed SPM 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
Z compressed ECAT i image
Z compressed ECAT v image
Z compressed GIS image
Z compressed SPM image
Zeiss czi

Associated ontology rules

  • brainvisa-3.2.0 :
    • {center}/{subject}/anatomical_mri/{acquisition}/{analysis}/segmentation/brain_<subject>
  • flat :
    • ./brain_<filename>

    Key attributes

  • brainvisa-3.0 :
    • protocol ,  subject ,  filename_variable ,  acquisition
  • brainvisa-3.1.0 :
    • protocol ,  subject ,  acquisition ,  analysis ,  side
  • brainvisa-3.2.0 :
    • rescan ,  time_duration ,  time_point ,  acquisition_date ,  center ,  subject ,  acquisition ,  analysis ,  acquisition_sequence ,  processing ,  side ,  mapped ,  contrast
  • 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