Summary of what happened:
I got nipype.pipeline.engine.nodes.NodeExecutionError while running fmriprep. Do any of you know how to fix it? Thank you so much!
Command used (and if a helper script was used, a link to the helper script or the command generated):
/opt/conda/envs/fmriprep/bin/fmriprep /Shared/PBS_JiangLab/Bingfang/pilot/bidsdata /Shared/PBS_JiangLab/Bingfang/pilot/fmriprep participant --participant-label 01 --output-spaces MNI152NLin2009cAsym:res-2 --stop-on-first-crash --use-plugin /Shared/PBS_JiangLab/Bingfang/pilot/scripts/plugin.yml --ignore slicetiming --fs-license-file /Shared/PBS_JiangLab/Bingfang/code/license.txt --resource-monitor --low-mem --force-bbr --anat-only -w /Shared/PBS_JiangLab/Bingfang/pilot/workdir
Version:
23.1.4
Environment (Docker, Singularity, custom installation):
Singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
File Path: 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”.
Type: Warning
File: sub-01_task-number_run-1_bold.nii.gz
Location: bidsdata/sub-01/func/sub-01_task-number_run-1_bold.nii.gz
Reason: Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /events.tsv, /task-number_events.tsv, /run-1_events.tsv, /task-number_run-1_events.tsv, /sub-01/sub-01_events.tsv, /sub-01/sub-01_task-number_events.tsv, /sub-01/sub-01_run-1_events.tsv, /sub-01/sub-01_task-number_run-1_events.tsv, /sub-01/func/sub-01_events.tsv, /sub-01/func/sub-01_task-number_events.tsv, /sub-01/func/sub-01_run-1_events.tsv, /sub-01/func/sub-01_task-number_run-1_events.tsv
Type: Warning
File: sub-01_task-number_run-2_bold.nii.gz
Location: bidsdata/sub-01/func/sub-01_task-number_run-2_bold.nii.gz
Reason: Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /events.tsv, /task-number_events.tsv, /run-2_events.tsv, /task-number_run-2_events.tsv, /sub-01/sub-01_events.tsv, /sub-01/sub-01_task-number_events.tsv, /sub-01/sub-01_run-2_events.tsv, /sub-01/sub-01_task-number_run-2_events.tsv, /sub-01/func/sub-01_events.tsv, /sub-01/func/sub-01_task-number_events.tsv, /sub-01/func/sub-01_run-2_events.tsv, /sub-01/func/sub-01_task-number_run-2_events.tsv
======================================================
File Path: The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification.
Type: Warning
======================================================
Relevant log outputs (up to 20 lines):
Node Name: fmriprep_23_1_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.inu_n4
File: /Shared/PBS_JiangLab/Bingfang/pilot/fmriprep/sub-01/log/20230909-144303_ca8d7a02-5b79-4135-9724-b698f811045e/crash-20230909-190221-bingfhuang-inu_n4-a3e40891-5ddd-4568-8d92-4c3aabb715f1.txt
Working Directory: /Shared/PBS_JiangLab/Bingfang/pilot/workdir/fmriprep_23_1_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/inu_n4
Inputs:
args:
bias_image:
bspline_fitting_distance: 200.0
bspline_order:
convergence_threshold: 1e-07
copy_header: True
dimension: 3
environ: {‘NSLOTS’: ‘8’}
histogram_sharpening:
input_image: [‘/Shared/PBS_JiangLab/Bingfang/pilot/workdir/fmriprep_23_1_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/truncate_images/mapflow/_truncate_images0/sub-01_T1w_noise_corrected_maths.nii.gz’]
mask_image:
n_iterations: [50, 50, 50, 50]
num_threads: 8
output_image:
rescale_intensities: False
save_bias: False
shrink_factor: 4
weight_image:
Traceback (most recent call last):
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/legacymultiproc.py”, line 67, in run_node
result[“result”] = node.run(updatehash=updatehash)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 527, in run
result = self._run_interface(execute=True)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 1380, in _run_interface
result = self._collate_results(
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 1249, in _collate_results
for i, nresult, err in nodes:
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/utils.py”, line 94, in nodelist_runner
result = node.run(updatehash=updatehash)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 527, in run
result = self._run_interface(execute=True)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 645, in _run_interface
return self._run_command(execute)
File “/opt/conda/envs/fmriprep/lib/python3.10/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 _inu_n40.
Cmdline:
N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /Shared/PBS_JiangLab/Bingfang/pilot/workdir/fmriprep_23_1_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/truncate_images/mapflow/_truncate_images0/sub-01_T1w_noise_corrected_maths.nii.gz --convergence [ 50x50x50x50, 1e-07 ] --output sub-01_T1w_noise_corrected_maths_corrected.nii.gz --shrink-factor 4
Stdout:
Stderr:
Killed
Traceback:
Traceback (most recent call last):
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py”, line 453, in aggregate_outputs
setattr(outputs, key, val)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py”, line 330, in validate
value = super(File, self).validate(objekt, name, value, return_pathlike=True)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py”, line 135, in validate
self.error(objekt, name, str(value))
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/traits/base_trait_handler.py”, line 74, in error
raise TraitError(
traits.trait_errors.TraitError: The ‘output_image’ trait of a N4BiasFieldCorrectionOutputSpec instance must be a pathlike object or string representing an existing file, but a value of ‘/Shared/PBS_JiangLab/Bingfang/pilot/workdir/fmriprep_23_1_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-01_T1w_noise_corrected_maths_corrected.nii.gz’ was specified.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 398, in run
runtime = self._post_run_hook(runtime)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/mixins/fixheader.py", line 127, in _post_run_hook
outputs = self.aggregate_outputs(runtime=runtime).get_traitsfree()
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 460, in aggregate_outputs
raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory '/Shared/PBS_JiangLab/Bingfang/pilot/workdir/fmriprep_23_1_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-01_T1w_noise_corrected_maths_corrected.nii.gz'
When creating this crashfile, the results file corresponding
to the node could not be found.