MRIQC trouble with multiecho data?

[jameswyngaarden]

What happened?

When running MRIQC I'm getting the following error message, which seems to only occur for multiecho data:

TypeError: expected str, bytes or os.PathLike object, not list

Thank you

What command did you use?

TEMPLATEFLOW_DIR=/ZPOOL/data/tools/templateflow
export APPTAINERENV_TEMPLATEFLOW_HOME=/opt/templateflow
singularity run --cleanenv \
-B ${TEMPLATEFLOW_DIR}:/opt/templateflow \
-B $maindir:/base \
-B $scratchdir:/scratch \
/ZPOOL/data/tools/mriqc-24.0.0.simg \
/base/bids /base/derivatives/mriqc \
participant --participant_label $sub \
-w /scratch

What version of the software are you running?

24.0.0

How are you running this software?

Singularity

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

Process Process-2:
Traceback (most recent call last):
  File "/opt/conda/lib/python3.11/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/opt/conda/lib/python3.11/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/opt/conda/lib/python3.11/site-packages/mriqc/cli/workflow.py", line 56, in build_workflow
    retval['workflow'] = init_mriqc_wf()
                         ^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/mriqc/workflows/core.py", line 48, in init_mriqc_wf
    workflow.add_nodes([fmri_qc_workflow()])
                        ^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/mriqc/workflows/functional/base.py", line 90, in fmri_qc_workflow
    bold_len = nb.load(bold_path).shape[3]
               ^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/nibabel/loadsave.py", line 96, in load
    filename = _stringify_path(filename)
               ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/nibabel/filename_parser.py", line 41, in _stringify_path
    return pathlib.Path(filepath_or_buffer).expanduser().as_posix()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/pathlib.py", line 871, in __new__
    self = cls._from_parts(args)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/pathlib.py", line 509, in _from_parts
    drv, root, parts = self._parse_args(args)
                       ^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/pathlib.py", line 493, in _parse_args
    a = os.fspath(a)
        ^^^^^^^^^^^^
TypeError: expected str, bytes or os.PathLike object, not list

Additional information / screenshots

No response

[effigies]

Duplicate of #1282. This will be fixed in the next release.

[caaam3]

I also have the same problem. Is there any solution for it?

Thanks!