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cpp-lln-lab / CPP_HPC

https://cpp-lln-lab.github.io/CPP_HPC/
MIT License
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freesurfer don't generate rh.sphere.reg file #25

Open yyang1234 opened 10 months ago

yyang1234 commented 10 months ago

I encountered an error while running FMRIPrep on a cluster. It appears that FreeSurfer attempted to open a file named rh.sphere.reg, but this file is missing. This issue has been observed in two separate subjects. details for job.txt are as follows


    SUBJECTS_DIR    /output/sourcedata/freesurfer
    FREESURFER_HOME /opt/freesurfer
    Loading source label.
    Found 3962 points in source label.
    Starting surface-based mapping
    Reading source registration 
     /output/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg
    error: No such file or directory
    error: MRISread(/output/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg): could not open file
    ERROR: could not read /output/sourcedata/freesurfer/fsaverage/surf/rh.sphere.reg
    Linux lm3-w045.cluster 3.10.0-1160.71.1.el7.x86_64 #1 SMP Tue Jun 28 15:37:28 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

    recon-all -s sub-04 exited with ERRORS at Fri Nov  3 12:59:16 CET 2023

    For more details, see the log file /output/sourcedata/freesurfer/sub-04/scripts/recon-all-rh.log
    To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Stderr:

Traceback:
    RuntimeError: subprocess exited with code 1.

231103-12:59:21,780 cli ERROR:
     Preprocessing did not finish successfully. Errors occurred while processing data from participants: 04 (1). Check the HTML reports for details.
231103-13:03:11,40 nipype.workflow INFO:
     [Node] Finished "_parcstats0", elapsed time 314.132945s.
yyang1234 commented 10 months ago

Hi, here's some update. The error disappeared after I cleared the content in both the output folder and the scratch folder.