Fmriprep sentry error but finally "fmriPrep finished successfully" in the output with image

Software Support
1

Summary of what happened:

Hi, there. I’m a beginner of fmriPrep.
I got a problem of sentry error, which is like in the following picture. The output file repeats different things failed to run on host bnode29 but finally successful with data(see relevant log outputs).
I don’t know what this means and what I can do. I was also wondering what was happening here, what cli error means and if the image data processed correct.
Thanks for help.

Command used (and if a helper script was used, a link to the helper script or the command generated):

singularity run --cleanenv /home1/data/toolbox/fmriprep/fmriprep-20.2.7.simg BIDS OUTPUT participant --participant-label SUBID --skip_bids_validation --nprocs 20 --force-bbr --fs-license-file /home1/data/toolbox/freesurfer/license.txt --fs-no-reconall -w OUTPUT/tmp --output-spaces MNI152NLin6Asym:res-2 fsaverage

Version: 20.2.7

Environment (Docker, Singularity / Apptainer, custom installation): Singularity

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

When creating this crashfile, the results file corresponding
to the node could not be found.
250728-03:00:30,511 nipype.workflow ERROR:
	 Node ds_report_summary failed to run on host bnode29.
250728-03:00:30,524 nipype.workflow ERROR:
	 Saving crash info to /home1/data/OpenfMRI_data/preprocessed/ds005604/fmriprep/sub-wlsubj123/log/20250728-025143_22a57bbb-ec7c-47db-aa8e-ff64654a9c75/crash-20250728-030030-data-ds_report_summary-5c141c5a-eefc-44cc-b25e-b7fc7a437f98.txt
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers
    self.procs[jobid].run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 498, in run
    emptydirs(outdir, noexist_ok=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/utils/filemanip.py", line 799, in emptydirs
    raise ex
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/utils/filemanip.py", line 781, in emptydirs
    shutil.rmtree(path)
  File "/usr/local/miniconda/lib/python3.7/shutil.py", line 485, in rmtree
    _rmtree_safe_fd(fd, path, onerror)
  File "/usr/local/miniconda/lib/python3.7/shutil.py", line 443, in _rmtree_safe_fd
    onerror(os.unlink, fullname, sys.exc_info())
  File "/usr/local/miniconda/lib/python3.7/shutil.py", line 441, in _rmtree_safe_fd
    os.unlink(entry.name, dir_fd=topfd)
FileNotFoundError: [Errno 2] No such file or directory: '_0xe8c6d7477340e2deee1e9fc4a84e85e1.json'

250728-03:00:30,792 nipype.workflow ERROR:
	 Node ds_report_bold_conf failed to run on host bnode29.
250728-03:00:30,800 nipype.workflow ERROR:
	 Saving crash info to /home1/data/OpenfMRI_data/preprocessed/ds005604/fmriprep/sub-wlsubj123/log/20250728-025143_22a57bbb-ec7c-47db-aa8e-ff64654a9c75/crash-20250728-030030-ISTBI_data-ds_report_bold_conf-ae13e5f7-0523-496f-a79b-9c64f35fe04b.txt
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers
    self.procs[jobid].run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 498, in run
    emptydirs(outdir, noexist_ok=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/utils/filemanip.py", line 799, in emptydirs
    raise ex
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/utils/filemanip.py", line 781, in emptydirs
    shutil.rmtree(path)
  File "/usr/local/miniconda/lib/python3.7/shutil.py", line 485, in rmtree
    _rmtree_safe_fd(fd, path, onerror)
  File "/usr/local/miniconda/lib/python3.7/shutil.py", line 443, in _rmtree_safe_fd
    onerror(os.unlink, fullname, sys.exc_info())
  File "/usr/local/miniconda/lib/python3.7/shutil.py", line 441, in _rmtree_safe_fd
    os.unlink(entry.name, dir_fd=topfd)
FileNotFoundError: [Errno 2] No such file or directory: '_0x0a83ef0dc13058fa6ee22f2c4a8633b5.json'


When creating this crashfile, the results file corresponding
to the node could not be found.
250728-03:00:32,286 nipype.workflow IMPORTANT:
	 fMRIPrep finished successfully!
250728-03:00:32,300 nipype.workflow IMPORTANT:
	 Works derived from this fMRIPrep execution should include the boilerplate text found in <OUTPUT_PATH>/fmriprep/logs/CITATION.md.
250728-03:00:40,526 cli ERROR:
	 Preprocessing did not finish successfully. Errors occurred while processing data from participants: wlsubj123 (99). Check the HTML reports for details.

In fact, there are quite more such “failed to run on host nodexx”, I just copy two of them.

Screenshots / relevant information:

.err file

image
image1466×254 20.8 KB

2

Hi @FreyaWen and welcome to neurostars!

Please do not delete the software support post template in the future. I have added it back in for you and you can edit your post to provide the requested information.

In addition, it would be good to know what resources (memory, cpu) you are devoting to the job.

If you see the desc-preproc nifti image in your output, then you are likely good to go.

Best,
Steven

1 Like
4

Hi Steven,

Thank you very much for your help and for adding the template back. My apologies for not using it; I didn’t realize it was a required part of the post.I have edited the post and filled out the requested information.

Regarding the resources, I am using 20 CPU cores and I allocated 100G of memory to the job.

As for the output, I have checked and I can confirm that the desc-preproc nifti image is present in the output folder.

Best,
Freya

5

Hi @FreyaWen,

I think you’re good to go then! Although I’d recommend updating fmriprep to a newer version.

Best,
Steven

1 Like
6

Hi Steven,

Thanks for your response. If I understand it right, that is to say the sentry error in the .err file could be ignored? I asked for the AI Gemini to figure out this problem, and I got an answer of the mechanism of slurm, which means “fMRIPrep finished successfully” stands for successful completion. But I’m still wondering what’s the meaning of cli error: Preprocessing did not finish successfully. Errors occurred while processing data from participants: wlsubj123 (99). Check the HTML reports for details. Could you please help me understand what this means?

Best,
Freya

7

Hi @FreyaWen,

The sentry error often means there was insufficient memory. But I would wait until any error replicates on newer fmriprep versions before investigating further.

Best,
Steven

8

Hi Steven,

Thanks for your advice. I’ll check it later!

Best,
Freya