Thank you!

So, I followed your suggestion and I edited the wm.mgz, filled.mgz, and the brain.finalsurfs.manedit.mgz.

First, I got this result (see the attached picture below) which I was happy about.

But the next time, when I edited the data the same way using another participant, I received this:

Screen Shot 2025-02-03 at 1.49.59 PM.png

My question is: how can I make the red line/pial surface not stop "too early" and reach the edge? I just want to delete the wrongly categorized white matter voxels and make them belong to the gray matter. I think when I edit/delete the wm voxels in the brain.finalsurfs.manedit.mgz, that stops the pial surface but that did not happen on the first figure. I am not sure what caused the difference.

Also, sometimes even when I delete/edit the white matter, the white matter surface/blue line still does not change.

Am I doing something wrong with recon-all maybe? (I use recon-all -autorecon2-wm -autorecon3)

Screen Shot 2025-02-03 at 2.28.55 PM.png

Thank you again!

Douglas N. Greve <dgreve@mgh.harvard.edu> ezt írta (időpont: 2025. jan. 23., Cs, 8:37):

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:
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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.

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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