Thanks, Doug!


I think we were probably going about this the wrong way. If I transform the ROI from MNI space back into native space, will the following commands give the proper cortical thickness extraction from native space?

mri_vol2surf --mov roi_in_native_space.nii.gz --out rh.roi_in_native_space.mgh --hemi rh --regheader ${subj}

#Check surface placement with:
tksurfer ${subj} rh inflated -overlay rh.roi_in_native_space.mgh -fthresh 1  

cd $FSdir/$subj/surf
mri_segstats --seg /path_to rh.roi_in_native_space.mgh --in rh.thickness --sum segstats-rh.roi_ns.txt

Thanks,


Dan