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