It looks like you ran into system compatibility issues. Your recon-all.log
shows that you are running centos6 release on Linux 9 machine. See this thread
for related discussions
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg74552.html
Yujing
From: Samantha Hendry <shend...@ed.ac.uk>
Sent: Friday, July 11, 2025 1:54 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: Freesurfer output. Segmentation fault (core dumped)
during parcellation step
External Email - Use Caution
Hi,
That’s is great thank you I will check it out sorry I think I gave you the
wrong scripts here is a different one from this year fi this would make anymore
sense thankyou! 😊
Best wishes
Samantha
From: fsbuild <fsbu...@contbay.com<mailto:fsbu...@contbay.com>>
Sent: 10 July 2025 22:16
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: Freesurfer output. Segmentation fault (core dumped)
during parcellation step
External Email - Use Caution
This posting indicates that changing the path to ./stats from ../stats got rid
of a segmentation fault. I would at least check that all paths in the
arguments ro mris_anatomical_stats are correct though.
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg10245.html<https://secure-web.cisco.com/1kII4TbCI49cZwwlOnHYFCUUaBglX8r7MQeqWDAa8DZ2GU4lEmYKOj_wbneyDbhaMjrSuD55XqcKpCtU_iuqlsEO_2fEr5F6Tu41whj0LnOvCI19zUC-wKVfcUxLuFs--dCTtM522Sdifs5dPqGb8Wx82Cc36u-16hr9ywCoylr26iyEQZp3nw0TzaoQ3beB_LZ7iOtWUE6KiGlFTpHnzymOvDt7sI02XGGpxixQ1k2jbYhR4Ef8hoyA-oxeYL38TDbLIqBA8aQz6rdwLChdsEvVJUKnCKI7h39V_5pBnimewrmf9JJZiAC3pU4h-xQKlS5HnXdYsny9sqYdnPCpsQA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg10245.html>
But I don’t see the error in the recon -all log you sent which is apparently
from May 2020 showing Freesurfer 6.0.0 is being run on RedHat Enterprise Linux
7.5.
- R.
On Jul 10, 2025, at 16:24, Samantha Hendry
<shend...@ed.ac.uk<mailto:shend...@ed.ac.uk>> wrote:
mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c
../label/aparc.annot.ctab FMS_0094 lh white
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