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, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIF image, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, VIDA image, Ventana bif, XBM image, XPM image, Zeiss czi, gz compressed MINC image, gz compressed NIFTI-1 image

GW_interface :

gz compressed NIFTI-1 image, Aperio svs, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIF image, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, VIDA image, Ventana bif, XBM image, XPM image, 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, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image

sulci_voronoi :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image