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
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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: image.png]
But the next time, when I edited
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
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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 "
