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
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