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Hi everyone,

I hope you're all doing well!

I'm running into a bit of trouble with some manual adjustments to our segmentation results and was wondering if anyone has encountered something similar. After running recon-all, I noticed that the white and pial surfaces aren’t aligning properly with the brain mask—especially around the motor areas where some white and gray matter seem to be missing.

I went ahead and edited the white matter (wm.mgz) file and ran autorecon2-wm. Normally, this runs through the steps from -normalization2 to -curvstats, stated in this site: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags. However, it stopped after the -fix stage, so I had to run remaining commands one by one. That worked out fine for the white surface.

Now, for the pial surfaces, I ran autorecon3, but I got this error:

reading surface from ../surf/lh.white.preaparc...
error: No such file or directory
error: mrisReadTriangleFile opened ../surf/lh.sphere.reg okay but surface doesn't match ../surf/lh.white.preaparc. nvertices:246347 != mris->nvertices:135204 || nfaces:492690 != mris->nfaces:270404
error: No such file or directory
error: mrisReadTriangleFile failed.
error: No such file or directory
error: mris_jacobian: could not read target surface ../surf/lh.sphere.reg
Linux compute-11 4.18.0-513.18.1.el8_9.x86_64 #1 SMP Wed Feb 21 21:34:36 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s freesurfer exited with ERRORS at Thu Feb 20 17:32:52 CET 2025

Any advice or insights on how to move forward would be much appreciated.

Thanks a lot!

Best,
Asli