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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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@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
 
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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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of hmarzban@student.ubc.ca
Sent: Thursday, March 13, 2025 7:47 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Unusual Cortical Thickness Measurements

 

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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