Split Brain Mask

Split the brain into three parts (hemispheres + cerebellum)

Description

This procedure aims at splitting the two hemispheres and at removing the cerebellum and a part of brain stem in order to give access to the internal and low faces of the cortex.
An erosion is applied to a mask of white matter in order to split it at the levels of corpus callosum and pons. This operation provides 3 seeds corresponding to the two hemispheres and cerebellum. Then, these seeds grow first inside white matter and finally throughout grey matter in order to recover the hemisphere shapes.

Parameters

brain_mask: T1 Brain Mask ( input )

t1mri_nobias: T1 MRI Bias Corrected ( input )

histo_analysis: Histo Analysis ( input )

commissure_coordinates: Commissure coordinates ( optional, input )

use_ridges: Boolean ( input )

white_ridges: T1 MRI White Matter Ridges ( input )

use_template: Boolean ( input )

split_template: Hemispheres Template ( input )

mode: Choice ( input )

variant: Choice ( input )

bary_factor: Choice ( input )

between 0 and 1.

mult_factor: Choice ( optional, input )

initial_erosion: Float ( input )

cc_min_size: Integer ( input )

split_brain: Split Brain Mask ( output )

fix_random_seed: Boolean ( input )

Technical information

Toolbox : Morphologist

User level : 0

Identifier : SplitBrain

File name : brainvisa/toolboxes/morphologist/processes/segmentationpipeline/components/SplitBrain.py

Supported file formats :

brain_mask :

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

t1mri_nobias :

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

histo_analysis :

Histo Analysis, Histo Analysis

commissure_coordinates :

Commissure coordinates, Commissure coordinates

white_ridges :

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

split_template :

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

split_brain :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image