It depends on how you do the transform back to native space. You can view the roi on the volume in the native space to see whether it landed in the right place and that the surface goes through it

doug

ps. Please remember to include previous correspondences

On 02/28/2018 07:29 PM, Albrecht, Daniel S. wrote:

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

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