sorry about this, one more iteration yet. I believe the files that you sent me are subject-specific .annot files (resampled to each subject cortical tessellation, and typically located in each subject label folder), please enter in CONN instead (and send me if CONN is not able to load them) the reference lh.aparc*.annot files (defined in fsaverage space, and typically located in freesurfer fsaverage folder). In case of doubt, you can tell whether a particular .annot file is in fsaverage space simply because the number of vertices will be exactly 163842 (in each hemisphere), while subject-specific .annot files have any arbitrary number of vertices. You can check the number of vertices in a freesurfer annotation file using the syntax:

   fname = 'lh.aparc.DKTatlas.annot';
   fp = fopen(fname,'r','b');
   n = fread(fp,1,'int');
   fclose(fp);
   fprintf('%d vertices in %s\n',n,fname);


Best
Alfonso


Originally posted by Amy Bouchard: