So is the problem that cortex is 2000 every where including your label or is it that it is 2000 away from you label and you want it to be 0? Note that unlabeled cortical voxels will come out at 2000 (for rh) and 1000 (for lh). Your labels should come out at 1000+N or 2000+N
doug
Martin Kavec wrote:
Hi,
I have a problem using mri_aparc2aseg with a custom annotations containing labels created manually in tksurfer and exported.
Basically, I would like to end up with a volume file similar as aparc+aseg.mgz but containing only a strip of a cortex corresponding to a label defined using tksurfer. The command I used is following:
mri_aparc2aseg --s fsaverage --o labels.mgz --anot labels
The command passes fine, but what I get is 2000 for all the cortical voxels, while I expected zeros for all the cortical voxels, except for those corresponding to the label. Any help on is greatly appreciated.
Thanks,
Martin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer