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We are running fmriprep on a dataset composed by two different sessions, each one with two tasks and two resting-state. Each task has 5 runs.
The pipeline crashes when doing the N4BiasFieldCorrection. Anyone knows why is this happening?
The error reported is referring only to one run but it happens for all of them.
I also tried to run fmriprep with and without the -u $UID flag
240618-14:28:42,669 nipype.workflow INFO:
[Node] Finished "n4_correct", elapsed time 6.519346s.
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/cli/run.py", line 155, in main
fmriprep_wf.run(**config.nipype.get_plugin())
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/base.py", line 178, in run
self._clean_queue(jobid, graph, result=result)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/base.py", line 256, in _clean_queue
raise RuntimeError("".join(result["traceback"]))
RuntimeError: Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/legacymultiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node n4_correct.
Cmdline:
N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /tmp/work/fmriprep_23_2_wf/sub_04_wf/bold_ses_post_task_semanticpost_run4_wf/bold_fit_wf/hmc_boldref_wf/gen_avg/sub-04_ses-post_task-semanticpost_run4_bold_average.nii.gz --output sub-04_ses-post_task-semanticpost_run4_bold_average_corrected.nii.gz -r --weight-image /tmp/tpl-MNI152NLin2009cAsym_res-01_label-brain_probseg_trans_fixhdr.nii.gz
Stdout:
Stderr:
Traceback:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 453, in aggregate_outputs
setattr(outputs, key, val)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate
value = super(File, self).validate(objekt, name, value, return_pathlike=True)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
self.error(objekt, name, str(value))
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/traits/base_trait_handler.py", line 74, in error
raise TraitError(
traits.trait_errors.TraitError: The 'output_image' trait of a _FixN4BiasFieldCorrectionOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/tmp/work/fmriprep_23_2_wf/sub_04_wf/bold_ses_post_task_semanticpost_run4_wf/bold_fit_wf/enhance_and_skullstrip_bold_wf/n4_correct/sub-04_ses-post_task-semanticpost_run4_bold_average_corrected.nii.gz'<class 'str'> was specified.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 398, in run
runtime = self._post_run_hook(runtime)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/mixins/fixheader.py", line 127, in _post_run_hook
outputs = self.aggregate_outputs(runtime=runtime).get_traitsfree()
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 460, in aggregate_outputs
raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory '/tmp/work/fmriprep_23_2_wf/sub_04_wf/bold_ses_post_task_semanticpost_run4_wf/bold_fit_wf/enhance_and_skullstrip_bold_wf/n4_correct/sub-04_ses-post_task-semanticpost_run4_bold_average_corrected.nii.gz'for output 'output_image' of a FixN4BiasFieldCorrection interface
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/bin/fmriprep", line 8, in<module>sys.exit(main())
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/cli/run.py", line 217, in main
failed_reports = generate_reports(
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/reports/core.py", line 96, in generate_reports
report_errors = [
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/reports/core.py", line 97, in<listcomp>
run_reports(
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/reports/core.py", line 86, in run_reports
).generate_report()
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/niworkflows/reports/core.py", line 435, in generate_report
(self.out_dir / self.out_filename).write_text(report_render, encoding="UTF-8")
File "/opt/conda/envs/fmriprep/lib/python3.10/pathlib.py", line 1154, in write_text
with self.open(mode='w', encoding=encoding, errors=errors, newline=newline) as f:
File "/opt/conda/envs/fmriprep/lib/python3.10/pathlib.py", line 1119, in open
return self._accessor.open(self, mode, buffering, encoding, errors,
PermissionError: [Errno 13] Permission denied: '/out/sub-04.html'
fMRIPrep: Please report errors to https://github.com/nipreps/fmriprep/issues
Additional information / screenshots
No response
The text was updated successfully, but these errors were encountered:
@mariagiuliat I noticed that your BOLD files do not follow BIDS format. You have run<number> in the filenames instead of run-<number>. Can you try fixing that?
As for the N4BiasFieldCorrection failure, I would recommend trying to follow the debugging steps taken in #3307- specifically @effigies' instructions in #3307 (comment).
What happened?
We are running fmriprep on a dataset composed by two different sessions, each one with two tasks and two resting-state. Each task has 5 runs.
The pipeline crashes when doing the N4BiasFieldCorrection. Anyone knows why is this happening?
The error reported is referring only to one run but it happens for all of them.
I also tried to run fmriprep with and without the -u $UID flag
This is my bids tree:
Thank you!
What command did you use?
What version of fMRIPrep are you running?
fMRIPrep-23.2.1
How are you running fMRIPrep?
Docker
Is your data BIDS valid?
Yes
Are you reusing any previously computed results?
No
Please copy and paste any relevant log output.
Additional information / screenshots
No response
The text was updated successfully, but these errors were encountered: