I’m encountering this strange error while using version 21.0.2
Node Name: fmriprep_wf.single_subject_C501_wf.func_preproc_ses_1post_task_VerbNback_run_1_wf.unwarp_wf.brainextraction_wf.clipper_pre
File: /N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/fmriprep-21.0.2/sub-C501/log/20220705-181654_396a0ce4-6943-4879-816a-91cff124252a/crash-20220706-123925-dlevitas-clipper_pre-a2dcd77e-9c6f-4088-bc63-273854dde356.txt
Working Directory: /N/scratch/dlevitas/fmriprep-21.0.2_temp/sub-C501/fmriprep_wf/single_subject_C501_wf/func_preproc_ses_1post_task_VerbNback_run_1_wf/unwarp_wf/brainextraction_wf/clipper_pre
Inputs:
dtype: int16
in_file:
invert: False
nonnegative: True
p_max: 99.98
p_min: 35.0
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/niworkflows/interfaces/nibabel.py", line 409, in _run_interface
self._results["out_file"] = _advanced_clip(
File "/opt/conda/lib/python3.8/site-packages/niworkflows/interfaces/nibabel.py", line 543, in _advanced_clip
a_min = np.percentile(
File "<__array_function__ internals>", line 5, in percentile
File "/opt/conda/lib/python3.8/site-packages/numpy/lib/function_base.py", line 3818, in percentile
return _quantile_unchecked(
File "/opt/conda/lib/python3.8/site-packages/numpy/lib/function_base.py", line 3937, in _quantile_unchecked
r, k = _ureduce(a, func=_quantile_ureduce_func, q=q, axis=axis, out=out,
File "/opt/conda/lib/python3.8/site-packages/numpy/lib/function_base.py", line 3515, in _ureduce
r = func(a, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/numpy/lib/function_base.py", line 4050, in _quantile_ureduce_func
n = np.isnan(ap[-1])
IndexError: index -1 is out of bounds for axis 0 with size 0
My fmriprep command is:
unset PYTHONPATH; singularity run \
-B ${bids_root_dir}:${bids_root_dir} \
-B /N/dcwan/projects/irf/templateflow:/opt/templateflow
-B ${work_dir}:${work_dir} \
-B ${output_dir}:${output_dir} \
/N/dcwan/projects/irf/containers/fmriprep-${fmriprep_version}.simg \
$bids_root_dir $output_dir \
participant \
--participant-label $s \
--task-id $task_id \
--skip-bids-validation \
--md-only-boilerplate \
--fs-license-file $FREESURFER_HOME/license.txt \
--fs-subjects-dir $output_dir/sourcedata/freesurfer/sub-${s} \
--output-spaces MNI152NLin6Asym:res-2 \
--nthreads $cores \
--stop-on-first-crash \
--resource-monitor \
--low-mem \
--mem_mb $reduced_mem \
--use-plugin $bids_root_dir/fmriprep_plugin_${s}.yml \
--use-aroma \
--use-syn-sdc \
--verbose \
--output-layout bids \
-w $work_dir/sub-${s}
This dataset is different from previous datasets I’ve worked with, in that this contains 2 sessions (each session has a T1w
image) and doesn’t contain field maps, so I’m using the --use-syn-sdc
parameter. I haven’t been able to find this error message online, so I was wondering what might be causing this issue?