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Update and rename 05_make_wm_mask.m to zero5_make_wm_mask.m #13

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Update and rename 05_make_wm_mask.m to zero5_make_wm_mask.m #13

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37 changes: 0 additions & 37 deletions Concussion/05_make_wm_mask.m
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37 changes: 37 additions & 0 deletions Concussion/zero5_make_wm_mask.m
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Original file line number Diff line number Diff line change
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% This script makes the white-matter mask used to track the connectomes in
% Caiafa and Pestilli Manuscript.
%
% Input is the parcellated and segmented white matter mask from freesurfer segmentation
% (github.com/brain-life/pestillilab_projects/Concussion/freesurfer_segmentation), subject (subj), and anatomy
% directory (anatomypath).
%
% Output will be wmMask.nii.gz file. This will be used in mrtrix tracking
% (github.com/brain-life/pestillilab_projects/zero6_ensemble_tractography).
%
% 2017 Brad Caron Indiana University, Pestilli Lab

% Get the base directory for the data; edit for your data and file structure
anatomypath = '/N/dc2/projects/lifebid/Concussion/concussion_test';
subjects = '1_005';

wmMaskFile = fullfile(anatomypath,subjects{isbj},'diffusion_data', '1000', 'Anatomy', 'wmMask.nii.gz');
fs_wm = fullfile(anatomypath,subjects{isbj},'diffusion_directory', 'Anatomy', 'aparc+aseg.nii.gz');
fprintf('\n loading %s \n',fs_wm);
wm = niftiRead(fs_wm);
wm.fname = wmMaskFile;
invals = [2 41 16 17 28 60 51 53 12 52 13 18 54 50 11 251 252 253 254 255 10 49 46 7];
origvals = unique(wm.data(:));
fprintf('\n[%s] Converting voxels... ',mfilename);
wmCounter=0;noWMCounter=0;
for ii = 1:length(origvals);
if any(origvals(ii) == invals)
wm.data( wm.data == origvals(ii) ) = 1;
wmCounter=wmCounter+1;
else
wm.data( wm.data == origvals(ii) ) = 0;
noWMCounter = noWMCounter + 1;
end
end
fprintf('converted %i regions to White-matter (%i regions left outside of WM)\n\n',wmCounter,noWMCounter);
niftiWrite(wm);
end