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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:
https://secure-web.cisco.com/1AUk84tBnT0XsxZ2iOt4m3Vg71XkMkCLnMtpqtMs1crG4WBGOxAZWklJJHxKt030IH5p0obvte6yvky_WjS7l-sV-1nnOfUix-QlpYaOaN58qAh0La0sq4JELWz1C86fBag-NmihdpZIt2eiy-Aq254HvV3Zw1jJfrj1EB_joKxRSijaDdxOW7TlJ1-faAVBqAvdew9l4jGAkZIkOs6PVx0m2I5VoCkt30xZ54VnWYoDGStMkKd3X01aKD5Ayx62KF5m8aZHXghFRVy5UEOE7qcxx-D9Ur1zXe0wIIEAHqwrZK-KamOtiP-8G3RlL7ZsQxpwfgYAfiPAfs1ANX_c_kw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FOtherUsefulFlags
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
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