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