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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of hmarzban@student.ubc.ca hmarzban@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

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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