It looks like it failed to create the fsaverage symbolic link in your SUBJECTS_DIR.
It looks like your SUBJECTS_DIR=/mfs/cvl/groups/rugg/ruggdata/UTD/EXPT2/FMR/fmri102/freesurfer/ss. Can you check if 'fsaverage' already exits in your SUBJECTS_DIR? If so, remove it and re-run recon-all. Also, remove '-parallel' from recon-all command line. Use '-threads 4' instead.
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Sambamoorthy, Sowmya Sent: Thursday, September 19, 2024 12:59 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] BA1_exvivo does not exist in SUBJECTS_DIR fsaverage
External Email - Use Caution Hello Freesurfer support,
We have freesurfer/7.3.2 on CentOS7. This installation is working fine and the recons (recon-all -autorecon-pial -s $SUBJECT -parallel) run to completion.
What we are trying to do:
Upgrade OS to ROCKY Linux 8.10. and trying to make freesurfer/7.3.2 work to completion.The reason we are keeping 7.3.2 is to not add variance to the current project.
What issue we are facing: <<snippet of the last few lines of the log below>>
Reporting on 45 segmentations Using PrintSegStat mri_segstats done /mfs/cvl/groups/rugg/ruggdata/UTD/EXPT2/FMR/fmri102/freesurfer/ss/fmri102_005_rocky/label INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject...
cd /mfs/cvl/groups/rugg/ruggdata/UTD/EXPT2/FMR/fmri102/freesurfer/ss; ln -s /opt/freesurfer/7.3.2/freesurfer/subjects/fsaverage; cd -
ln: failed to create symbolic link './fsaverage': File exists #-------------------------------------------- #@# BA_exvivo Labels lh Wed Sep 11 17:06:02 CDT 2024 ------------------------------------------------------------------------- ERROR: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage! The fsaverage link probably points to an older freesurfer version ------------------------------------------------------------------------- Linux rocky8-sg.cvl.utdallas.edu 4.18.0-553.8.1.el8_10.x86_64 #1 SMP Tue Jul 2 17:10:26 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s fmri102_005_rocky exited with ERRORS at Wed Sep 11 17:06:02 CDT 2024
More Context:
1. The same brain on Centos7 has no issues finishing recons. If needed, we can share logs for this. 2. We have tried adding some fsaverage switches as seen on a few support groups. "recon-all -autorecon-pial -s $SUBJECT -parallel --fs-subjects-dir $SUBJECTS_DIR". This does not seem to help and does not get past the initial phases of the run.
Hope this helps in giving the picture of what we are attempting to accomplish. Please let me know if you have any questions.
--Sowmya
Sowmya Sambamoorthy Research Assistant (972) 883-3746 Functional Neuroimaging of Memory Laboratory [cid:image001.png@01DB0A97.40C8C300] T H E U N I V E R S I T Y O F T E X A S A T D A L L A S
