I don’t see any errors in the attached log.
I noticed that you specified ‘-parallel’ in your recon-all. It is the parallelism done at recon-all level. There is no synchronization mechanism to guard shared sources accessing. There have been reports of ‘ln -s’ errors due to that. I’m wondering if it is the case here even though no detailed errors reported in recon-all.log
It doesn’t look like that your recon-all finished running. It seems to have stopped at ‘Surface Registration’. I think you need to rerun recon-all from AUTORECON 3 with directive ‘-autorecon3’. Remove ‘-parallel’ flag.
‘recon-all’ steps are described in this wiki page https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Quah, Bryan Sent: Thursday, February 27, 2025 1:06 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Unknown error when running longitudinal analysis
External Email - Use Caution Hello FreeSurfer Enthusiasts,
I'm attempting to run longitudinal analysis, as described here MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorialhttps://secure-web.cisco.com/1afGGFCyfveweaeVugpgH1DSg-Q9U8pxbe-yGl2q4FZoab5WhVdxvNswIxvsGRXAs2e3Db31OWL9g3A-K3PiotGwHUtxXZFVacX-0xO1UBXgFSCiP6hSr554njPNsdcbEtElBCJiimPwcjgVDuGtZFRpCCDS-B2PwSMAX-C4nz8g2iQnuuuBq-nPRl5M7yV4ZCvXqGm35oUfFiREGWxByla_9mw7Z7Dvn0jErp8e0P_4vmIszafFNozLTBjIvRzKZ0qgY4PZOPr3PFoMWOq3RGw76ec7XthzTjPtMd7-rn14hG76AeSasLBmasb3El7HISImZzyu94aA-X-xxJOr2wA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FLongitudinalTutorial. I am able to run the CROSS and BASE analyses without any errors logged, but running the LONG analysis produces an error message at the end of the process:
"recon-all -s CID220_20211116.long.CID220 exited with ERRORS at Mon Feb 17 22:26:11 PST 2025"
I ran this process with the command "recon-all -long CID220_20211116 CID220 -all -parallel -openmp 12". I have also looked through the recon-all.log file but could not find anything describing the error. I have attached the log file and hopefully you will be able to find it useful. Could anyone help troubleshoot the log file to see if there is an error during processing? Or is there a way I could verify if the longitudinal analysis process ran correctly based on produced output masks/metrics?
More details:
1) FreeSurfer version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b 2) Platform: Ubuntu 20.04.6 LTS 3) uname -a: Linux titan2 5.13.0-39-generic #44~20.04.1-Ubuntu SMP Thu Mar 24 16:43:35 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached
Thanks, Bryan Quah
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