I would also be helpful to have some pics of what you are seeing. The surface is not valid in the "medial well" -- ie all the non-cortical structures on the central sagittial plane such as thalamus an VDC.

On 1/16/2024 7:50 AM, Huang, Yujing wrote:

Can you try the troubleshooting methods from this page:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData

Best,

Yujing

*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Sunniva Fenn-Moltu *Sent:* Monday, January 15, 2024 6:35 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Midline white/pial surface

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Hi,

i'm running recon-all and have encountered an issue with the surface boundaries on several subjects. What I'm experiencing is that the midline surface is included in the white surface in one hemisphere, and in the pial surface on the other hemisphere. This results in the midline boundary of the thalamus and ventral DC being white surface in one hemisphere, and pial surface in the other. Do you have any idea why this is happening?

I am running freesurfer on NoMachine (freesurfer/7.4.1).

Best,

Sunniva

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