Hi, that's very strange, but I wasn't able to reproduce this with the subjects in which this happened. I made a new subject with the same MRI and this time it all behaved as expected... maybe it's because I did it through the GUI this time? Usually I use this code to automate it:
for nSubject = 1:length(existing_subjects)-1
% Load subject to get info
indexN = find(contains(names,existing_subjects(nSubject).name));
selectedEEG = ids{indexN};
selectedGroup = groups{indexN};
sFiles = [existing_subjects(nSubject).name '\' selectedGroup '\data_temp_0001.mat'];
% If segmentation has already been done, skip
if isfile([folder_anat existing_subjects(nSubject).name '\tess_cortex_central_low.mat'])
continue
end
% Process: Segment MRI with CAT12
sFiles = bst_process('CallProcess', 'process_segment_cat12', sFiles, [], ...
'subjectname', existing_subjects(nSubject).name, ...
'nvertices', 15000, ...
'tpmnii', {'', 'Nifti1'}, ...
'sphreg', 1, ...
'vol', 1, ...
'extramaps', 0, ...
'cerebellum', 0);
% Save and display report
ReportFile = bst_report('Save', sFiles);
bst_report('Open', ReportFile);
end