Hi Lisa, are you trying to skull strip in order to do something outside of freesurfer or are you trying to troubleshoot a freesurfer failure? If you want to run the skull stripping by itself, you can run the mri_watershed program.

doug

Lisa F. Akiyama wrote:

Hello FreeSurfers,

By reading through the wiki, it seems like the skullstrip command uses nu.mgz and T1.mgz,
but is there a way to just run the skullstrip command without nuintensitycor or normalization?
I have MRIs of a few subjects in which the intensity normalization seems to not have beneficial for preparing the MRIs for skullstripping.
I've attached the snapshot of brainmask.mgz to this email.

Thanks in advance.


Best,
Lisa
 ______________________________
Lisa F. Akiyama
Research Study Assistant
Institute for Learning & Brain Sciences (I-LABS)
University of Washington

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