Hemisphere Sulci Thickness and Volumes

Calcluation of cortical thickness descriptors in a cortical folds graph

Description

Cortical thickness descriptors are computed on the grey matter volume of each fold zone. Folds zones are the result of a Voronoi diagram, so are a parcellation of the whole cortex.
Thickness is calculated using a distance map (using a fast marching algorithm) between both cortex interfaces (grey/CSF and grey/white), and averaged on each fold zone (we also keep a standard deviation descriptor). As we use a binary segmentation for the grey matter, we are not using very smart methods for this calculation: this is certainly not the best possible method for thickness calculation, but a kind of robustness is achieved via the averaging of all voxels on the mid-interface between the CSF and white matter...

Parameters

graph: Cortical folds graph ( input )

hemi_cortex: CSF+GREY Mask ( input )

GW_interface: Grey White Mask ( input )

white_mesh: Hemisphere White Mesh ( input )

hemi_mesh: Hemisphere Mesh ( input )

output_graph: Cortical folds graph ( output )

write_mid_interface: Boolean ( input )

output_mid_interface: Grey White Mid-Interface Volume ( optional, output )

sulci_voronoi: Sulci Voronoi ( optional, input )

Technical information

Toolbox : Morphologist

User level : 2

Identifier : CorticalFoldsGraphThickness

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

Supported file formats :

graph :

Graph and data, Graph and data

hemi_cortex :

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

GW_interface :

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

white_mesh :

GIFTI file, GIFTI file, MESH mesh, MNI OBJ mesh, PLY mesh, TRI mesh

hemi_mesh :

GIFTI file, GIFTI file, MESH mesh, MNI OBJ mesh, PLY mesh, TRI mesh

output_graph :

Graph and data, Graph and data

output_mid_interface :

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

sulci_voronoi :

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