pandas.errors.EmptyDataError: No columns to parse from file

[dlevitas]

What happened?

I'm re-processing some data (originally processed using version 20.2.0), and am hitting this error during the acompcor confounds renaming procedure. This appears to be the same error as #2659.

What command did you use?

unset PYTHONPATH; singularity run \
-B /N/project/bold_perception/LoST:/N/project/bold_perception/LoST \
-B /N/dcwan/projects/irf/templateflow:/opt/templateflow \
-B /N/scratch/dlevitas/fmriprep-21.0.1_temp:/N/scratch/dlevitas/fmriprep-21.0.1_temp \
-B /N/project/bold_perception/LoST/derivatives/fmriprep-21.0.1:/N/project/bold_perception/LoST/derivatives/fmriprep-21.0.1 \
/N/dcwan/projects/irf/containers/fmriprep-21.0.1.simg \
/N/project/bold_perception/LoST \
/N/project/bold_perception/LoST/derivatives/fmriprep-21.0.1 \
participant \
--participant-label 10 \
--skip-bids-validation \
--md-only-boilerplate \
--fs-license-file /N/soft/rhel7/freesurfer/6.0.0/freesurfer/license.txt \
--fs-subjects-dir /N/project/bold_perception/LoST/derivatives/freesurfer-6.0.0 \
--output-spaces MNI152NLin2009cAsym:res-2 MNI152NLin6Asym:res-2 \
--use-aroma \
--nthreads 8 \
--stop-on-first-crash \
--resource-monitor \
--low-mem \
--mem_mb 30000 \
--use-plugin /N/project/bold_perception/LoST/fmriprep_plugin_10.yml \
--verbose \
--output-layout bids \
-w /N/scratch/dlevitas/fmriprep-21.0.1_temp/sub-10

What version of fMRIPrep are you running?

21.0.1

How are you running fMRIPrep?

Singularity

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

Node: fmriprep_wf.single_subject_10_wf.func_preproc_task_lost_run_3_wf.bold_confounds_wf.rename_acompcor
Working directory: /N/scratch/dlevitas/fmriprep-21.0.1_temp/sub-10/fmriprep_wf/single_subject_10_wf/func_preproc_task_lost_run_3_wf/bold_confounds_wf/rename_acompcor

Node inputs:

components_file = <undefined>
metadata_file = <undefined>

Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/legacymultiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run
    runtime = self._run_interface(runtime)
  File "/opt/conda/lib/python3.8/site-packages/fmriprep/interfaces/confounds.py", line 139, in _run_interface
    components = pd.read_csv(self.inputs.components_file, sep='\t')
  File "/opt/conda/lib/python3.8/site-packages/pandas/io/parsers.py", line 610, in read_csv
    return _read(filepath_or_buffer, kwds)
  File "/opt/conda/lib/python3.8/site-packages/pandas/io/parsers.py", line 462, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/opt/conda/lib/python3.8/site-packages/pandas/io/parsers.py", line 819, in __init__
    self._engine = self._make_engine(self.engine)
  File "/opt/conda/lib/python3.8/site-packages/pandas/io/parsers.py", line 1050, in _make_engine
    return mapping[engine](self.f, **self.options)  # type: ignore[call-arg]
  File "/opt/conda/lib/python3.8/site-packages/pandas/io/parsers.py", line 1873, in __init__
    self._reader = parsers.TextReader(self.handles.handle, **kwds)
  File "pandas/_libs/parsers.pyx", line 521, in pandas._libs.parsers.TextReader.__cinit__
pandas.errors.EmptyDataError: No columns to parse from file

Additional information / screenshots

This error has [currently] only occurred for a specific subject's run. The other subject's runs, and other subjects in general, are not hitting this error, though I will update if that becomes the case. I can't discern anything idiosyncratic about this run, so I'm unsure why it's failing here specifically.

[effigies]

Is this data multi-echo?

I believe it's a masking issue. If you have a subject that reliably hits this, would you be willing to share their data privately?

[dlevitas]

Not multi-echo, but it has a MultibandAccelerationFactor of 8 and has a corresponding SBRef file, for what it's worth.

Yes, if the issue persists I can share the data privately

[dlevitas]

Downgraded fmriprep version to 20.2.3 for now, but will reopen if I encounter this error again.