NoneType object error when running fmriprep on HPC using Singularity

Summary of what happened:

I am hitting an error when trying to run fMRIPrep on my university’s HPC cluster. fMRIPrep runs for the normal amount of time that it ran for when I ran it on my local computer (using the same dataset, and it ran smoothly), but at the end, it says it hit an error during preprocessing (see relevant log outputs for the error log). Is this error something to be concerned about or can we move forward with analyses?

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

This is the command that I ran using .sh scripts and submitting as a job:

singularity run --cleanenv -B /exports/eddie/scratch/$USER/ \

/exports/chss/eddie/ppls/groups/RichardsonLab/my_images/fmriprep-22.1.1.simg \

/exports/eddie/scratch/$USER/pixar/ /exports/eddie/scratch/$USER/pixar/derivatives \

participant --participant-label pixar001 --fs-license-file /home/s2461137/scripts/freesurfer.txt \

--nthreads 16 --omp-nthreads 16 --skip_bids_validation --fs-no-reconall --ignore slicetiming \

--fd-spike-threshold 2 --dvars-spike-threshold 3

Version:

fmriprep 22.1.1

Environment (Docker, Singularity, custom installation):

Using Singularity on university HPC Cluster.

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

The BIDS validator gives three warnings:

**Warning 1: [Code 25] EVENTS_TSV_MISSING**
Task scans should have a corresponding events.tsv file. If this is a resting state scan you can ignore this warning or rename the task to include the word "rest".

**Warning 2: [Code 39] INCONSISTENT_PARAMETERS**
Not all subjects/sessions/runs have the same scanning parameters.

**Warning 3: [Code 82] CUSTOM_COLUMN_WITHOUT_DESCRIPTION**
Tabular file contains custom columns not described in a data dictionary

Relevant log outputs (up to 20 lines):

Traceback (most recent call last):
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers
    self.procs[jobid].run(updatehash=updatehash)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.9/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 summary.

Traceback:
	Traceback (most recent call last):
	  File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 398, in run
	    runtime = self._run_interface(runtime)
	  File "/opt/conda/lib/python3.9/site-packages/fmriprep/interfaces/reports.py", line 133, in _run_interface
	    return super(SubjectSummary, self)._run_interface(runtime)
	  File "/opt/conda/lib/python3.9/site-packages/fmriprep/interfaces/reports.py", line 96, in _run_interface
	    segment = self._generate_segment()
	  File "/opt/conda/lib/python3.9/site-packages/fmriprep/interfaces/reports.py", line 168, in _generate_segment
	    counts = Counter(
	  File "/opt/conda/lib/python3.9/collections/__init__.py", line 593, in __init__
	    self.update(iterable, **kwds)
	  File "/opt/conda/lib/python3.9/collections/__init__.py", line 679, in update
	    _count_elements(self, iterable)
	  File "/opt/conda/lib/python3.9/site-packages/fmriprep/interfaces/reports.py", line 169, in 
	    BIDS_NAME.search(series).groupdict()['task_id'][5:] for series in bold_series
	TypeError: 'NoneType' object is not subscriptable

Screenshots / relevant information:

What does your dataset look like?

@effigies, I’m using this dataset: OpenNeuro

Do you have a crashfile that was generated by the failing node? That might help.

Yes! Here are the contents of the crashfile:

Node: fmriprep_22_1_wf.single_subject_pixar001_wf.summary
Working directory: /exports/eddie3_homes_local/s2461137/work/fmriprep_22_1_wf/single_subject_pixar001_wf/summary

Node inputs:

bold = ['/exports/eddie/scratch/s2461137/pixar/sub-pixar001/func/sub-pixar001_func_sub-pixar001_task-pixar_bold.nii.gz', '/exports/eddie/scratch/s2461137/pixar/sub-pixar001/func/sub-pixar001_task-pixar_bold.nii.gz']
nstd_spaces = []
std_spaces = ['MNI152NLin2009cAsym']
subject_id = pixar001
subjects_dir = <undefined>
t1w = ['/exports/eddie/scratch/s2461137/pixar/sub-pixar001/anat/sub-pixar001_T1w.nii.gz', '/exports/eddie/scratch/s2461137/pixar/sub-pixar001/anat/sub-pixar001_anat_sub-pixar001_T1w.nii.gz']
t2w = <undefined>

Traceback (most recent call last):
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers
    self.procs[jobid].run(updatehash=updatehash)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.9/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 summary.

Traceback:
	Traceback (most recent call last):
	  File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 398, in run
	    runtime = self._run_interface(runtime)
	  File "/opt/conda/lib/python3.9/site-packages/fmriprep/interfaces/reports.py", line 133, in _run_interface
	    return super(SubjectSummary, self)._run_interface(runtime)
	  File "/opt/conda/lib/python3.9/site-packages/fmriprep/interfaces/reports.py", line 96, in _run_interface
	    segment = self._generate_segment()
	  File "/opt/conda/lib/python3.9/site-packages/fmriprep/interfaces/reports.py", line 168, in _generate_segment
	    counts = Counter(
	  File "/opt/conda/lib/python3.9/collections/__init__.py", line 593, in __init__
	    self.update(iterable, **kwds)
	  File "/opt/conda/lib/python3.9/collections/__init__.py", line 679, in update
	    _count_elements(self, iterable)
	  File "/opt/conda/lib/python3.9/site-packages/fmriprep/interfaces/reports.py", line 169, in <genexpr>
	    BIDS_NAME.search(series).groupdict()['task_id'][5:] for series in bold_series
	TypeError: 'NoneType' object is not subscriptable

These files have been modified and now have sub-pixar001_func_ prepended to the filename.