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Error occured in skullstrip_first_pass #545

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hyangjung-lee opened this issue Apr 21, 2023 · 0 comments
Open

Error occured in skullstrip_first_pass #545

hyangjung-lee opened this issue Apr 21, 2023 · 0 comments
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bug Something isn't working

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@hyangjung-lee
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hyangjung-lee commented Apr 21, 2023

What happened?
Hi! I'm testing this pipeline for a single subject (My BIDS folder contains only one subject's data).
I replaced the original T1 file with neck-stripped T1w.
I just realized that an error occurred at the stage of "skullstrip_first_pass".

Is there an error message?
As far as I can tell from the log file (both log.txt file and
err.txt text file attached), it's basically FileNotFoundError?
When I checked out one nii.gz file associated with the error, it was present in the mentioned folder but appears to be an alias.
*.nii.gz file path: ../nipype/fmriprep_wf/single_subject_0004_wf/func_preproc_ses_4_task_Resting_run_1_wf/initial_boldref_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected.nii.gz

I guess this is why the problematic file in the log file was not found.
*.pklz file path:
..skullstrip_first_pass/result_skullstrip_first_pass.pklz

In contrast, a file we expect from the stage (n4_correct) right before "skullstrip_first_pass", seems OK to me when I read it in fsleyes.
*.nii.gz file path:
../n4_correct/ref_bold_corrected.nii.gz

What is the exact command that you used to run Halfpipe?
docker run --interactive --tty --volume /:/ext halfpipe/halfpipe --workdir myWDPATH

Which settings did you use?
The jsonspec.txt) file is attached.

If you need any more information, please let me know.
Thanks in advance for your help.

@hyangjung-lee hyangjung-lee added the bug Something isn't working label Apr 21, 2023
@HippocampusGirl HippocampusGirl removed their assignment May 13, 2024
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