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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.
The text was updated successfully, but these errors were encountered:
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.
The text was updated successfully, but these errors were encountered: