Skip to content

freesurfer don't generate rh.sphere.reg file #25

@yyang1234

Description

@yyang1234

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.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions