Hi Doug,

I'm trying to skull strip in order to do something outside of freesurfer. Thanks - I will try running mri_watershed.

Best, Lisa ______________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington E-mail: lrisa87@uw.edu

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On Tue, Nov 30, 2010 at 9:51 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:

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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