BIDS validation for fMRIPrep-rodents

Summary of what happened:

Using fMRIprep-rodent. Validate data on online BIDS-validator. Passes without errors. Try to use fMRIprep-rodents tool. Get what I assume is BIDS-related error.

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

docker run -ti --rm -v /Users/kelvin/Library/CloudStorage/OneDrive-DanmarksTekniskeUniversitet/Thesis/thesis_git/data/data_bids/rsfMRI_example_bids:/bids_dataset:ro -v /Users/kelvin/Library/CloudStorage/OneDrive-DanmarksTekniskeUniversitet/Thesis/thesis_git/data/data_processed:/outputs nipreps/fmriprep-rodents:fmri_prep_rodent /bids_dataset /outputs participant -w /work



  • building docker image from current github repo locally
  • docker pull latest

Environment (Docker, Singularity, custom installation):

  • Docker
  • Custom docker

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

As mentioned, passes test on online validator. I get a few warnings, but no errors

Relevant log outputs (up to 20 lines):

Traceback (most recent call last):
  File "/opt/conda/bin/fprodents", line 8, in <module>
  File "/opt/conda/lib/python3.8/site-packages/fprodents/cli/", line 17, in main
  File "/opt/conda/lib/python3.8/site-packages/fprodents/cli/", line 634, in parse_args
  File "/opt/conda/lib/python3.8/site-packages/fprodents/utils/", line 148, in validate_input_dir
    subprocess.check_call(["bids-validator", bids_dir, "-c",])
  File "/opt/conda/lib/python3.8/", line 364, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['bids-validator', PosixPath('/bids_dataset'), '-c', '/tmp/tmpaghsvbjh']' returned non-zero exit status 1.

Screenshots / relevant information:

There should have been output from the validator in addition to the Python traceback from calling out to it. Since the error is not FileNotFound, the validator is installed and should have produced some output.

Thank you for the swift reply!:slight_smile: I have managed to fix the issue. It was because I did not mount /bids_data, very silly. However, I now run into:

    Running fMRIPREP version 0.0.2+83.gd153551:
      * BIDS dataset path: /bids_dataset.
      * Participant list: ['01'].
      * Run identifier: 20230123-143151_7ab13fbc-46f3-4da5-8554-25049e8b72e1.
      * Output spaces: Fischer344:res-native.
Process Process-2:
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/multiprocessing/", line 315, in _bootstrap
  File "/opt/conda/lib/python3.8/multiprocessing/", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/opt/conda/lib/python3.8/site-packages/fprodents/cli/", line 81, in build_workflow
    retval["workflow"] = init_fmriprep_wf()
  File "/opt/conda/lib/python3.8/site-packages/fprodents/workflows/", line 50, in init_fmriprep_wf
    single_subject_wf = init_single_subject_wf(subject_id)
  File "/opt/conda/lib/python3.8/site-packages/fprodents/workflows/", line 246, in init_single_subject_wf
    anat_preproc_wf = init_anat_preproc_wf(
  File "/opt/conda/lib/python3.8/site-packages/fprodents/patch/workflows/", line 289, in init_anat_preproc_wf
    anat_template_wf = init_anat_template_wf(
  File "/opt/conda/lib/python3.8/site-packages/smriprep/workflows/", line 681, in init_anat_template_wf
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/freesurfer/", line 244, in __init__
    super(FSCommandOpenMP, self).__init__(**inputs)
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/freesurfer/", line 134, in __init__
    self.inputs.subjects_dir = self._subjects_dir
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/", line 135, in validate
    self.error(objekt, name, str(value))
  File "/opt/conda/lib/python3.8/site-packages/traits/", line 74, in error
    raise TraitError(
traits.trait_errors.TraitError: The 'subjects_dir' trait of a RobustTemplateInputSpec instance must be a pathlike object or string representing an existing directory, but a value of '/opt/freesurfer/subjects' <class 'str'> was specified.

And I have not been able to find anything online.

Hmm. This looks like a quirk of a FreeSurfer tool we use that always takes a subjects_dir input even if it doesn’t use it. The simplest thing might be to pass an environment variable SUBJECTS_DIR=/tmp.