I would not worry about it. It is just used to help exclude voxels for whitening.

Dan Dillon wrote:

Dear FreeSurfers,

I'm having some trouble with my brain masks. Below I have inserted a subject's T1.mgz and brain.nii overlay (made with preproc-sess). As you can see, the mask goes well beyond the boundaries of the brain. Any ideas what could cause this--perhaps noisy functional scans? The majority of my subjects' masks look like this.

Should I worry about this? My brainmask.mgz files are all fine, and I can use those to mask out voxels for visualization purposes--Do I need to be concerned if my brain.nii volumes look this way? Would I fix by running mkbrainmask-sess and tweaking the "-threshold" argument?

Thanks!

Dan Dillon

Affective Neuroscience Lab

Harvard University

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