That is a harder problem. I'm not sure what is causing that bright spot.
Artery? B0? The problem is that it is too bright and the algorithm says
"hey, that's not gray matter" and does not know what to do. You can
edit the voxel intensities in the brainmask.finalsurfs.manedit to darken
them so they look like cortex. I think it should work but not sure
On 2/3/2025 2:37 PM, Eszter Boros wrote:
External Email - Use Caution
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.
image.png
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 <dgr...@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.
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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