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