CAT doesn't provide Schaefer 7-Network Parcellation

pdhami · September 10, 2020, 1:08am

Dear Brainstorm Community,

I was hoping to use CAT to segment the MRIs of each individual participant, so I can get for each participant the 7-network Schaefer parcellation for their brain. However, after running CAT successfully, when I open up the individual cortex and the atlases load, the 7-network parcellations are missing (the 17-network parcellations are there however). Any ideas as to how to get the 7-network parcellation in this case?

Best,
Paul

Francois · September 12, 2020, 10:06am

It looks like newer versions of CAT12 do not include the 7-network parcellations, nor the 800 and 1000 ROIs parcellations.

@CGaser
I don't remember why I included such a long list of files in my import code (see below). Were there more .annot files available in the cat12 folder before?

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/io/import_anatomy_cat.m#L166


FsAvgRsphFile = bst_fullfile(CatExeDir, 'templates_surfaces', 'rh.sphere.freesurfer.gii');
Fs32kLsphFile = bst_fullfile(CatExeDir, 'templates_surfaces_32k', 'lh.sphere.freesurfer.gii');
Fs32kRsphFile = bst_fullfile(CatExeDir, 'templates_surfaces_32k', 'rh.sphere.freesurfer.gii');
% Find FSAverage labels in CAT12 program folder
AnnotAvgLhFiles = {file_find(bst_fullfile(CatExeDir, 'atlases_surfaces'), 'lh.aparc_a2009s.freesurfer.annot', 2), ...
                   file_find(bst_fullfile(CatExeDir, 'atlases_surfaces'), 'lh.aparc_DK40.freesurfer.annot', 2), ...
                   file_find(bst_fullfile(CatExeDir, 'atlases_surfaces'), 'lh.aparc_HCP_MMP1.freesurfer.annot', 2)};
AnnotAvgRhFiles = {file_find(bst_fullfile(CatExeDir, 'atlases_surfaces'), 'rh.aparc_a2009s.freesurfer.annot', 2), ...
                   file_find(bst_fullfile(CatExeDir, 'atlases_surfaces'), 'rh.aparc_DK40.freesurfer.annot', 2), ...
                   file_find(bst_fullfile(CatExeDir, 'atlases_surfaces'), 'rh.aparc_HCP_MMP1.freesurfer.annot', 2)};
Annot32kLhFiles = {file_find(bst_fullfile(CatExeDir, 'atlases_surfaces_32k'), 'lh.Schaefer2018_100Parcels_7Networks_order.annot', 2), ...
                   file_find(bst_fullfile(CatExeDir, 'atlases_surfaces_32k'), 'lh.Schaefer2018_100Parcels_17Networks_order.annot', 2), ...
                   file_find(bst_fullfile(CatExeDir, 'atlases_surfaces_32k'), 'lh.Schaefer2018_200Parcels_7Networks_order.annot', 2), ...
                   file_find(bst_fullfile(CatExeDir, 'atlases_surfaces_32k'), 'lh.Schaefer2018_200Parcels_17Networks_order.annot', 2), ...
                   file_find(bst_fullfile(CatExeDir, 'atlases_surfaces_32k'), 'lh.Schaefer2018_400Parcels_7Networks_order.annot', 2), ...
                   file_find(bst_fullfile(CatExeDir, 'atlases_surfaces_32k'), 'lh.Schaefer2018_400Parcels_17Networks_order.annot', 2), ...
                   file_find(bst_fullfile(CatExeDir, 'atlases_surfaces_32k'), 'lh.Schaefer2018_600Parcels_7Networks_order.annot', 2), ...
                   file_find(bst_fullfile(CatExeDir, 'atlases_surfaces_32k'), 'lh.Schaefer2018_600Parcels_17Networks_order.annot', 2), ...
                   file_find(bst_fullfile(CatExeDir, 'atlases_surfaces_32k'), 'lh.Schaefer2018_800Parcels_7Networks_order.annot', 2), ...
                   file_find(bst_fullfile(CatExeDir, 'atlases_surfaces_32k'), 'lh.Schaefer2018_800Parcels_17Networks_order.annot', 2), ...
                   file_find(bst_fullfile(CatExeDir, 'atlases_surfaces_32k'), 'lh.Schaefer2018_1000Parcels_7Networks_order.annot', 2), ...