Problem:
fmriprep crashed due to a NodeExecutionError when running fslstats for calc_median_val. This was run across 6 subjects and threw this error for the second subject, subsequently crashing fmriprep.
Error Log:
Node: fmriprep_22_1_wf.single_subject_06_wf.func_preproc_task_int_wf.ica_aroma_wf.calc_median_val
Working directory: /tmp/work/fmriprep_22_1_wf/single_subject_06_wf/func_preproc_task_int_wf/ica_aroma_wf/calc_median_val
Node inputs:
args = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
in_file = <undefined>
index_mask_file = <undefined>
mask_file = <undefined>
op_string = -k %s -p 50
output_type = NIFTI_GZ
split_4d = <undefined>
Traceback (most recent call last):
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.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 calc_median_val.
Cmdline:
fslstats /tmp/work/fmriprep_22_1_wf/single_subject_06_wf/func_preproc_task_int_wf/bold_std_trans_wf/_std_target_MNI152NLin6Asym.res2/merge/vol0000_xform-00000_clipped_merged_cut.nii.gz -k /tmp/work/fmriprep_22_1_wf/single_subject_06_wf/func_preproc_task_int_wf/bold_std_trans_wf/_std_target_MNI152NLin6Asym.res2/mask_std_tfm/vol0000_unwarped_merged_valid_average_corrected_brain_mask_maths_trans.nii.gz -p 50
Stdout:
Stderr:
Killed
Traceback:
RuntimeError: subprocess exited with code 137.
The command:
fmriprep-docker ~/Desktop/bids /datadisk/fmriprep participant --participant-label 05 06 07 08 09 10 --fs-license-file ~/Desktop/FreeSurfer/license.txt --skip-bids-validation --n-cpus 30 --use-aroma --output-spaces MNI152NLin6Asym:res-2
Version:
fMRIPrep 22.1.1
System:
Ubuntu 20.0.4
I have seen the NodeExecutionError for others that was linked to the FreeSurfer reconstruction. But this doesn’t look to be the case here (?). Does anyone have any ideas about this error and how to solve it?
UPDATE:
I have now tried running the subject that failed alone and without --use-aroma and got no errors. Is there a bug with ICA-AROMA or a different issues happening here?