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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