search

nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
631 stars 293 forks source link

N4BiasFieldCorrection fails on multiple run dataset #3314

Open mariagiuliat opened 3 months ago

mariagiuliat commented 3 months ago

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:

Nifti
├── CHANGES
├── README
├── dataset_description.json
├── participants.tsv
├── sub-01
│   └── ses-post
│   │   ├── anat
│   │    |   ├── sub-01_ses-post_T1w.json
│   │    |   └── sub-01_ses-post_T1w.nii.gz
│   │   └── func
│   │       ├── sub-01_ses-post_task-episodicpost_run1_bold.json
│   │       └── sub-01_ses-post_task-episodicpost_run1_bold.nii.gz
│   │       ├── sub-01_ses-post_task-episodicpost_run2_bold.json
│   │       └── sub-01_ses-post_task-episodicpost_run2_bold.nii.gz
│   │       ├── sub-01_ses-post_task-episodicpost_run3_bold.json
│   │       └── sub-01_ses-post_task-episodicpost_run3_bold.nii.gz
│   │       ├── sub-01_ses-post_task-episodicpost_run4_bold.json
│   │       └── sub-01_ses-post_task-episodicpost_run4_bold.nii.gz
│   │       ├── sub-01_ses-post_task-episodicpost_run5_bold.json
│   │       └── sub-01_ses-post_task-episodicpost_run5_bold.nii.gz
│   │       ├── sub-01_ses-post_task-semanticpost_run1_bold.json
│   │       └── sub-01_ses-post_task-semanticpost_run1_bold.nii.gz
│   │       ├── sub-01_ses-post_task-semanticpost_run2_bold.json
│   │       └── sub-01_ses-post_task-semanticpost_run2_bold.nii.gz
│   │       ├── sub-01_ses-post_task-semanticpost_run3_bold.json
│   │       └── sub-01_ses-post_task-semanticpost_run3_bold.nii.gz
│   │       ├── sub-01_ses-post_task-semanticpost_run4_bold.json
│   │       └── sub-01_ses-post_task-semanticpost_run4_bold.nii.gz
│   │       ├── sub-01_ses-post_task-semanticpost_run5_bold.json
│   │       └── sub-01_ses-post_task-semanticpost_run5_bold.nii.gz
│   │       ├── sub-01_ses-post_task-restpost_run1_bold.json
│   │       └── sub-01_ses-post_task-restpost_run1_bold.nii.gz
│   │       ├── sub-01_ses-post_task-restpost_run2_bold.json
│   │       └── sub-01_ses-post_task-restpost_run2_bold.nii.gz
│   └── ses-pre
│       ├── anat
│        |   ├── sub-01_ses-pre_T1w.json
│        |   └── sub-01_ses-pre_T1w.nii.gz
│       └── func
│           ├── sub-01_ses-pre_task-episodicpre_run1_bold.json
│           └── sub-01_ses-pre_task-episodicpre_run1_bold.nii.gz
│           ├── sub-01_ses-pre_task-episodicpre_run2_bold.json
│           └── sub-01_ses-pre_task-episodicpre_run2_bold.nii.gz
│           ├── sub-01_ses-pre_task-episodicpre_run3_bold.json
│           └── sub-01_ses-pre_task-episodicpre_run3_bold.nii.gz
│           ├── sub-01_ses-pre_task-episodicpre_run4_bold.json
│           └── sub-01_ses-pre_task-episodicpre_run4_bold.nii.gz
│           ├── sub-01_ses-pre_task-episodicpre_run5_bold.json
│           └── sub-01_ses-pre_task-episodicpre_run5_bold.nii.gz
│           ├── sub-01_ses-pre_task-semanticpre_run1_bold.json
│           └── sub-01_ses-pre_task-semanticpre_run1_bold.nii.gz
│           ├── sub-01_ses-pre_task-semanticpre_run2_bold.json
│           └── sub-01_ses-pre_task-semanticpre_run2_bold.nii.gz
│           ├── sub-01_ses-pre_task-semanticpre_run3_bold.json
│           └── sub-01_ses-pre_task-semanticpre_run3_bold.nii.gz
│           ├── sub-01_ses-pre_task-semanticpre_run4_bold.json
│           └── sub-01_ses-pre_task-semanticpre_run4_bold.nii.gz
│           ├── sub-01_ses-pre_task-semanticpre_run5_bold.json
│           └── sub-01_ses-pre_task-semanticpre_run5_bold.nii.gz
│           ├── sub-01_ses-pre_task-restpre_run1_bold.json
│           └── sub-01_ses-pre_task-restpre_run1_bold.nii.gz
│           ├── sub-01_ses-pre_task-restpre_run2_bold.json
│           └── sub-01_ses-pre_task-restpre_run2_bold.nii.gz
│
└── task-episodicpre_bold.json

Thank you!

What command did you use?

RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=26.1.3 -it -u 1003 \
    -v /media/data_1t/keepinmind/derivatives/license.txt:/opt/freesurfer/license.txt:ro \
    -v /media/data_1t/keepinmind:/data:ro \
    -v /media/data_1t/keepinmind/derivatives:/out \
    -v /media/data_1t/keepinmind/code/plugin.yml:/tmp/plugin.yml:ro \
    nipreps/fmriprep:23.2.1 \
    /data /out participant \
    --skip_bids_validation \
    --participant-label 04 \
    --stop-on-first-crash \
    --use-plugin /tmp/plugin.yml \
    --output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym

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.

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

tsalo commented 3 months ago

@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 https://github.com/nipreps/fmriprep/issues/3307#issuecomment-2173546548.