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poldracklab / tacc-openneuro

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ds000051-fmriprep: 177422 Segmentation fault #33

Closed jbwexler closed 1 year ago

jbwexler commented 1 year ago

Just for sub-03.

221013-23:06:59,933 nipype.workflow CRITICAL: fMRIPrep failed: 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 524, in run result = self._run_interface(execute=True) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 642, in _run_interface return self._run_command(execute) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command raise NodeExecutionError( nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node skullstrip_first_pass.

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/nipype/interfaces/fsl/preprocess.py", line 165, in _run_interface self.raise_exception(runtime) File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 686, in raise_exception raise RuntimeError( RuntimeError: Command: bet sub-03_task-abstractconcretejudgment_run-04_bold_average_corrected.nii.gz sub-03_task-abstractconcretejudgment_run-04_bold_average_correc ted_brain.nii.gz -f 0.20 -m Standard output: /opt/fsl-6.0.5.1/bin/bet failed during command:sub-03_task-abstractconcretejudgment_run-04_bold_average_corrected.nii.gz sub-03_task-abstract concretejudgment_run-04_bold_average_corrected_brain.nii.gz -f 0.20 -m Standard error: /opt/fsl-6.0.5.1/bin/bet: line 399: 177422 Segmentation fault ${FSLDIR}/bin/bet2 $IN $OUT $bet2opts Return code: 1

jbwexler commented 1 year ago

@effigies Any thoughts on this? I recently got a similar issue for one subject in ds000224-fmriprep

jbwexler commented 1 year ago

This was solved thanks to @effigies' solution:

/scratch1/03201/jbwexler/work_dir/fmriprep/ds000224_sub-MSC03/fmriprep_22_0_wf/single_subject_MSC03_wf/func_preproc_ses_func06_task_memoryfaces_wf/final_boldref_wf/enhance_and_skullstrip_bold_wf/n4_correct is corrupted. I tried re-running the command, and it seemed to work (generating test.nii.gz in that directory). I think if you delete that directory and re-run it should work.