Recurring "unexpected keyword argument 'skip_file_prefixes'" Error

[jwrobertson86]

What happened?

I've been trying to process a longitudinal fMRI dataset for a while now. Most of the issues I've run into have been fixable with more hard drive space but I don't understand how to handle this specific error, because it doesn't seem obviously tied to a lack of computing resources (i.e., drive space or memory).

What command did you use?

fmriprep-docker esmi_fMRI_long/ esmi_fMRI_long/derivatives/ participant -w ~/ext_hdd/temp/ --longitudinal --fs-license-file license.txt
RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=28.1.1+1 -it -v /home/jason/Documents/work/fmri/license.txt:/opt/freesurfer/license.txt:ro -v /home/jason/Documents/work/fmri/esmi_fMRI_long:/data:ro -v /home/jason/Documents/work/fmri/esmi_fMRI_long/derivatives:/out -v /home/jason/ext_hdd/temp:/scratch nipreps/fmriprep:25.1.1 /data /out participant --longitudinal -w /scratch

What version of fMRIPrep are you running?

25.1.1

How are you running fMRIPrep?

Docker

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

FreeSurfer, Anatomical derivatives, Work directory

Please copy and paste any relevant log output.

[Node] Error on "fmriprep_25_1_wf.sub_ESS38731375X_wf.bold_ses_05_task_rs_wf.carpetplot_wf.conf_plot" (/scratch/fmriprep_25_1_wf/sub_ESS38731375X_wf/bold_ses_05_task_rs_wf/carpetplot_wf/conf_plot)
250704-19:47:15,982 nipype.workflow ERROR:
	 Node conf_plot failed to run on host 149765c001e5.
250704-19:47:15,990 nipype.workflow ERROR:
	 Saving crash info to /out/sub-ESS38731375X/log/20250703-212238_31483d2f-a6eb-4694-b2d9-5715aa688093/crash-20250704-194715-root-conf_plot-b671f62f-b348-4944-9f2f-5fe1b84efb23.txt
Traceback (most recent call last):
  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run
    result = self._run_interface(execute=True)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface
    return self._run_command(execute)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 769, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node conf_plot.

Traceback:
	Traceback (most recent call last):
	  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/nipype/interfaces/base/core.py", line 401, in run
	    runtime = self._run_interface(runtime)
	              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/fmriprep/interfaces/confounds.py", line 591, in _run_interface
	    ).plot()
	      ^^^^^^
	  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/nireports/reportlets/modality/func.py", line 105, in plot
	    figure = plt.figure(figsize=(19.2, sum(height_ratios)))
	             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/matplotlib/pyplot.py", line 1033, in figure
	    _api.warn_external(
	  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/matplotlib/_api/__init__.py", line 391, in warn_external
	    warnings.warn(message, category, **kwargs)
	TypeError: _warn() got an unexpected keyword argument 'skip_file_prefixes'

Additional information / screenshots

I'm running this on a Linux laptop (Ubuntu 24.04.2 LTS), 12 cores, 16 GB RAM, partition currently has 57 GB free of 315 GB. There's 45 subjects with 175 total datapoints, of which only one has generated an HTML summary file to date, meaning presumably the other 44 still need one or more sessions to still be preprocessed.

I've been reusing everything I can because I assume that's the most efficient route, but if I can clear out old scratch files etc., that would definitely be useful to know.

Also, this error seems to occur when running many different modules, not just conf_plot specifically. I'd upload those logs as well but GitHub isn't allowing it.

[jwrobertson86]

crash-20250707-161023-root-conf_plot-c262c409-efc9-4225-87d0-2bd6ada62dd1.txt
crash-20250707-161015-root-conf_corr_plot-f784b72f-7343-4bb1-8d52-be91e1d13aa2.txt
crash-20250707-161011-root-rois_plot-e1babc8c-5e5d-45d4-b1ab-8a2adbc17161.txt
crash-20250707-161011-root-compcor_plot-7b7e3bf7-cac8-4f83-bebc-0415f762f860.txt
crash-20250707-161000-root-conf_plot-503c316e-3082-41e7-a66a-2947412862d4.txt
crash-20250707-160948-root-conf_corr_plot-1ed77390-a5cc-4c4e-81f8-e86d0636e319.txt
crash-20250707-160945-root-rois_plot-42b428d8-6682-467c-a872-e6f31ecf1df5.txt
crash-20250707-160945-root-compcor_plot-8b5d088c-aa12-407c-90f7-e7c8622b2459.txt
crash-20250707-160929-root-conf_plot-bbcc3f56-f567-4d82-8a78-2bd371a3e623.txt
crash-20250707-160920-root-conf_corr_plot-e0d54351-0ad4-4d96-99db-7a4ea327bc7b.txt
crash-20250707-160916-root-compcor_plot-6b338e6d-2026-44cd-8109-24b484111d76.txt
crash-20250707-160907-root-rois_plot-ab8daf5a-ddf3-475e-9349-c5a6a3ab3f64.txt
crash-20250707-160905-root-epi_t1_report-4fd675c4-53d5-43ac-acfc-b7f4a4180ba7.txt
crash-20250707-160831-root-norm_rpt.a0-4dcfe3f1-8fa1-4690-8d25-28f335dc9519.txt
crash-20250707-160821-root-epi_t1_report-08924645-5523-4020-85f7-99fc8bfcf876.txt
crash-20250707-150515-root-seg_rpt-cd2c5419-1da5-466f-954b-d0d26bf14f4d.txt
crash-20250707-150124-root-recon_report-9f9c5de4-384a-4c27-a1ba-92b37edeb67a.txt

Update: It was a permissions issue. These were all the files generated during a run that just crashed on me about 15 minutes ago.

[jwrobertson86]

One more update: After running the program again with --low-mem enabled, I was able to at least obtain a full error report without my OS dying along the way. It's attached from the first error I could spot about a minute before the final end. It's long, so hopefully it's useful.

July 9 error sequence.txt

What I'm seeing is the same error recurring throughout at the point where it's creating plots for many of the subjects, which is something I don't know how to disable. I don't know if that in turn is indicative of any data issues that site QC didn't pick up on, but that seems unlikely for this many subjects.

[miltoncamacho]

Looking a bit deeper into the issue, it looks like the issue comes from an overwriting of the warnings function that causes the break when matplotlib tries to use the python 3.12 compatible warnings function which contains **kwargs. The overwriten fmriprep/_warnings.py funtion does not accept **kwargs.