crushed during 'anat_wf:anat_create_summary'

[xingyu-liu]

Hi!

I've been recenely encountered with this error no for whatever datasets. Here is the error log for the sample dataset you provide.

ERROR ~ Error executing process > 'anat_wf:anat_create_summary (sub-01)'

Caused by:
Process anat_wf:anat_create_summary (sub-01) terminated with an error exit status (1)

Command executed:

qc_create_summary.py --bids_dir /data --subjects_dir /output/test_sample_deepprep/Recon --subject_id sub-01 --template_space "NONE" --qc_result_path /output/test_sample_deepprep/QC --deepprep_version 23.1.0 --nextflow_log /output/test_sample_deepprep/WorkDir/nextflow/.nextflow.log

Command exit status:
1

Command output:
240515-21:08:20,898 nipype.workflow INFO:
[Node] Setting-up "T1w_Reports_run_node" in "T1w_Reports_run_node".
240515-21:08:20,899 nipype.workflow INFO:
[Node] Executing "T1w_Reports_run_node" <reports.reports_node.TemplateDimensions>
240515-21:08:20,927 nipype.workflow INFO:
[Node] Finished "T1w_Reports_run_node", elapsed time 0.020078s.

Command error:
240515-21:08:20,898 nipype.workflow INFO:
[Node] Setting-up "T1w_Reports_run_node" in "T1w_Reports_run_node".
240515-21:08:20,899 nipype.workflow INFO:
[Node] Executing "T1w_Reports_run_node" <reports.reports_node.TemplateDimensions>
240515-21:08:20,927 nipype.workflow INFO:
[Node] Finished "T1w_Reports_run_node", elapsed time 0.020078s.
Traceback (most recent call last):
File "/opt/DeepPrep/deepprep/nextflow/bin/qc_create_summary.py", line 140, in
TemplateDimensions_run(args.subject_id, t1w_files, qc_result_path)
File "/opt/DeepPrep/deepprep/nextflow/bin/qc_create_summary.py", line 78, in TemplateDimensions_run
shutil.copyfile(Path(node_name) / 'report.html',
File "/usr/lib/python3.10/shutil.py", line 256, in copyfile
with open(dst, 'wb') as fdst:
FileNotFoundError: [Errno 2] No such file or directory: '/output/test_sample_deepprep/QC/sub-01/figures/sub-01_desc-templatedimensions_report.html'

Work dir:
/output/test_sample_deepprep/WorkDir/nextflow/c3/abb69ba18c7c4b10a8b667b2ac7dbc

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

-- Check '.nextflow.log' file for details

Any idea on this? Thanks!

Best,
Xingyu

[JChRoy]

Hi Xingyu,

I had the same issue by cloning pBFSLab/DeepPrep.git
Using git clone https://github.com/IndiLab/DeepPrep.git which does not have this process enables to move forward.

Best,
Jean-Charles

[xingyu-liu]

Got it. Thank you very much!