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