Just finished running fmriprep for a batch of 40 subjects and noticed that all subject-specific html reports were missing. I really like these reports for quality control purposes. I tried exploring what went wrong and here’s what I found:
-got an error at the very end of the processing workflow:
(copy pasting from the end of the console outputs:)
201031-00:48:57,914 nipype.workflow IMPORTANT:
fMRIPrep finished successfully!
201031-00:48:58,33 nipype.workflow IMPORTANT:
Works derived from this fMRIPrep execution should include the boilerplate text found in <OUTPUT_PATH>/fmriprep/logs/CITATION.md.
Traceback (most recent call last):
File "/usr/local/miniconda/bin/fmriprep", line 10, in <module>
sys.exit(main())
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 163, in main
packagename="fmriprep",
File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/reports/core.py", line 534, in generate_reports
for subject_label in subject_list
File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/reports/core.py", line 534, in <listcomp>
for subject_label in subject_list
File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/reports/core.py", line 514, in run_reports
reportlets_dir=reportlets_dir,
File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/reports/core.py", line 371, in generate_report
.findall((logs_path / "CITATION.html").read_text())[0]
IndexError: list index out of range
-looks like all components of the html reports have been generated successfully
-tried rerunning for only a single subject and with --report-only
flag. it threw the same error
I didn’t delete any temporary work outputs, I think they should all be there (unless fmriprep deletes older ones to free up space?)
Any help would be appreciated.