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:

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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

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