It was just an oversight on my part when I wrote the program. I've just updated the file in our repository and put a copy here: https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize You can also specify all the structures you want by using the --match flag
On 7/20/18 10:00 AM, John Anderson wrote:
External Email - Use Caution
Dear Freesurfer experts, I would like to inquire about the flag --subcort-gm in mri_binarize. It seems that the final product of this flag create a mask include the brain stem which is largely white matter. Why it was included in the subcortical gray matter structures?
Thanks for any clarification, john
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer