yes, that would be one way to fix it. Or you could play with the skull strip
parameters, but if it is just a little stretch over a few slices might be
easiest to just erase them and rerun.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of hmarz...@student.ubc.ca
<hmarz...@student.ubc.ca>
Sent: Monday, March 17, 2025 2:22 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Unusual Cortical Thickness Measurements
External Email - Use Caution
Hi Bruce,
I’ve attached the pial and WM surfaces for this subject.
Just to clarify—are you saying I should manually edit the voxels, set their
values to 0, then rerun Skull Strip and run these commands?
recon-all -subjid your_subject -skullstrip -clean-bm -gcareg -canorm -careg
-noskullstrip
recon-all -subjid your_subject -autorecon2-pial
Also, if we want to avoid manual corrections (since we have about 100 subjects
with this issue), do you think adding T2w to recon-all might help resolve it?
Thank you!
Hengameh
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD
<bfis...@mgh.harvard.edu>
Sent: March 13, 2025 4:49 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Unusual Cortical Thickness Measurements
[CAUTION: Non-UBC Email]
Hi Hengameh
What does the pial surface look like in the volume? If it is grabbing dura you
would erase it and rerun part of recon-all.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of hmarz...@student.ubc.ca
Sent: Thursday, March 13, 2025 7:47 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Unusual Cortical Thickness Measurements
External Email - Use Caution
Hello,
I hope you are well.
I was wondering if there is an easy way to correct for missegmentation of the
grey matter parcellation. For example, would it be possible to correct for the
overestimation of the pre-postcentral gyri (see picture below)? Since it seems
as if the parcellation is extending into the meninges.
Warmly,
Hengameh
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