Hi Ran

yes, mri_extract_label or mri_binarize --match should do the trick

cheers Bruce On Sun, 24 Nov 2013, Ran Xu wrote:

Dear Freesurfer experts, I got the aseg+aparc.mgz, and converted it into the individual T1 space. Now, I am wondering if there is a way to extract the single subcortical structure, like thalamus, from the converted aseg+aparc.mgz.  I already know the thalamus label, how to get thalamus.mgz file in this label. Could someone help me out?

Thank you very much!

Ran