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The output of fmriprep is incomplete #3332
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There's either a permissions issue or a concurrency issue. Are you running multiple subjects simultaneously with the same FreeSurfer directory? |
Hi @effigies I possibly run multiple subjects because I submitted the |
So what's happening is that you have an There's no real plausible way to protect against this in code. It's up to users not to call fMRIPrep in parallel in this situation. |
Hi @effigies It occurs an error later. This error is very strange. Sometimes I'm running fmriprep and I don't get this error, sometimes I run it and it keeps coming up. Is there any way to fix this? For example, submit a job first. After this job is completed, I submit the parallel array job. |
That sounds like a recurrence of the other issue you opened: #3258. |
Yes, it's an old problem. I tested it, and if I submit a job array for one subject, fmriprep (version-24.0.1) runs successfully with doing surface reconstruction. But if I submit a job array for multiple subjects, I get the error I mentioned above. By the way, the So, I'm ready to try this way: But I'm not sure it's the right thing to do. What do you think? @effigies |
What happened?
I used fmriprep-24.0.0 on
slurm
to process my MRI data, but the outputs were incomplete.For example,
freesurfer
directory was empty and the output of--output-space
I specified was not produced in thefunc
andanat
directory.I uploaded the log file. Please check it out
fmriprep-30459_6.json
What command did you use?
What version of fMRIPrep are you running?
24.0.0
How are you running fMRIPrep?
Singularity
Is your data BIDS valid?
Yes
Are you reusing any previously computed results?
No
Please copy and paste any relevant log output.
Additional information / screenshots
There are outputs in
func
directoryThe text was updated successfully, but these errors were encountered: