Thank you Bruce.
Does freesurfer use any binary label map during any processing steps?
Best Regards, Sarina
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, October 19, 2016 10:48 AM To: Freesurfer support list Subject: Re: [Freesurfer] Question regarding: Binary label map to skull strip brains
Hi Sarina
the skull stripping is done by combining a deformable surface with a watershed algorithm not with a label mask. The volume brainmask.mgz can be used to specify what is in brain (voxels >5) and what is not in brain (voxels < 5)
cheers Bruce
On Wed, 19 Oct 2016, Karmacharya, Sarina wrote:
Dear Freesurfer team,
I have a questions for you regarding the binary masks (labels maps) that freesufer uses to skull strip the brain in the first part of recon-all.
I was wondering if freesurfer stores/saves this label mask that it uses to skullstrip? If so what would be the naming convention of this label map/mask and the location of the label map/mask in the freesurfer folder.
I will be waiting to hear back from you.
Best Regards, Sarina
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