This is a known issue when recon-all v8-beta is run a 2nd time. It will be fixed in the final v8 release. In the mean time, you can get around it with cd $SUBJECTS_DIR/subject/surf mris_compute_lgi --i lh.pial mris_compute_lgi --i rh.pial
On 1/27/2025 5:59 AM, Katharina Wittfeld wrote:
External Email - Use Caution
Dear FreeSurfer Developers,
I'm attempting to compute the local gyrification index but unfortunately the calculations terminated with an error:
recon-all -subject XXX -localGI -hemi rh
FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta-20241102-b8aacdc
Platform used: Ubuntu 22.04.5 LTS
From the log file:
seg2cc --s XXX -rh
seg2cc: update not needed. Run with --force-update to force an update Command exited with non-zero status 1 @#@FSTIME 2025:01:23:19:41:20 seg2cc N 3 e 0.05 S 0.01 U 0.04 P 103% M 2916 F 0 R 2820 W 0 c 1 w 51 I 0 O 0 L 20.43 20.49 19.84 @#@FSLOADPOST 2025:01:23:19:41:20 seg2cc N 3 20.43 20.49 19.84 Linux gt-psych.med.uni-greifswald.de 5.15.0-130-generic #140-Ubuntu SMP Wed Dec 18 17:59:53 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s XXX exited with ERRORS at Thu Jan 23 19:41:20 CET 2025
The data was preprocessed before with recon-all and completed without any error and I've run this on multiple individuals without any success. The same commands worked fine with former FreeSurfer versions (6.0 and 7.3.2).
On the freesurfer mailing list I haven't detected this problem. I would be very greatful, if you have any idea how to run it in this new freesurfer version.
Best regards, Katharina
-- Dr. rer. nat. Katharina Wittfeld
University Medicine Greifswald Department of Psychiatry and Psychotherapy Ellernholzstr. 1/2 17475 Greifswald Germany
Tel. +49 3834 86 22166
e-mail:Katharina.Wittfeld@uni-greifswald.de
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