Attached is an image that describes my issue. WM in the temporal region is being omitted after running recon-all. Most of the omitted voxels are in the 120-130 range. It's causing an issue with the underlying WM voxels as well, they've simply disappeared.
I can see how this voxel intensity limit would help omit dura, vessels, and other high intensity objects but in this case it's a bit of an issue and I'm not sure how to A) rectify it (I could replace the WM voxels?) B) keep it from happening again. Is there a way to give freesurfer an intensity threshold to work with? Please advise! Jon
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