ds002322-fmriprep: "Segmentation fault ${FSLDIR}/bin/bet2 $IN $OUT $bet2opts"

Only happened for sub-45.

Node: fmriprep_wf.single_subject_45_wf.func_preproc_task_alice_echo_2_wf.final_boldref_wf.enhance _and_skullstrip_bold_wf.skullstrip_first_pass Working directory: /scratch1/03201/jbwexler/work_dir/fmriprep/ds002322_sub-45/fmriprepwf/single subject_45_wf/func_preproc_task_alice_echo_2_wf/final_boldref_wf/enhance_and_skullstrip_bold_wf/s kullstrip_first_pass

Node inputs:

args = center = environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'} frac = 0.2 functional = in_file = mask = True mesh = no_output = out_file = outline = output_type = NIFTI_GZ padding = radius = reduce_bias = remove_eyes = robust = skull = surfaces = t2_guided = threshold = vertical_gradient =

Traceback (most recent call last): File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.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/nipype/interfaces/fsl/preprocess.py", line 163, in _run_interface runtime = super(BET, self)._run_interface(runtime) File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 822, in _run _interface self.raise_exception(runtime) File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 749, in rais e_exception raise RuntimeError( RuntimeError: Command: bet vol0000_xform-00000_clipped_merged_average_corrected.nii.gz vol0000_xform-00000_clipped_merge d_average_corrected_brain.nii.gz -f 0.20 -m Standard output: /opt/fsl-6.0.5.1/bin/bet failed during command:vol0000_xform-00000_clipped_merged_average_correct ed.nii.gz vol0000_xform-00000_clipped_merged_average_corrected_brain.nii.gz -f 0.20 -m Standard error: /opt/fsl-6.0.5.1/bin/bet: line 399: 256984 Segmentation fault ${FSLDIR}/bin/bet2 $IN $OUT $b et2opts Return code: 1

poldracklab / tacc-openneuro

ds002322-fmriprep: "Segmentation fault ${FSLDIR}/bin/bet2 $IN $OUT $bet2opts" #15