You can edit the brain.finalsurfs.manedit.mgz to remove those voxels.
You may need to removed them from the wm.mgz and filled.mgz
On 1/21/2025 1:41 PM, Eszter Boros wrote:
External Email - Use Caution
Dear FreeSurfer Team,
We are editing some longitudinal data using FreeSurfer 7.4.1.
I am not sure how to fix the following issue (see the attached pictures).
The white surface (blue line) almost touches the pial surface because
some of the voxels are "too bright" at the edge, so they were
misidentified as white matter.
Screenshot 2025-01-21 at 1.21.23 PM.png
Screenshot 2025-01-21 at 1.21.32 PM.png
Which volume should I edit to fix this?
I was thinking about deleting these voxels from the brainmask but that
might lead to excluding/deleting gray matter incorrectly. Or maybe I
could delete these voxels from the white matter. I was also
considering cloning some of the surrounding voxels somehow to
make this area less bright.
Thank you,
Eszter
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