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ds003126-fmriprep: nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node _midthickness0. #31

Open jbwexler opened 1 year ago

jbwexler commented 1 year ago

Got this for every subject.

Node: _midthickness0 Working directory: /scratch1/03201/jbwexler/work_dir/fmriprep/ds003126_sub-047EPKL012074/fmriprep_22_0_wf/single_subject_047EPKL012074_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0

Node inputs:

args = distance = 0.5 dt = environ = {'SUBJECTS_DIR': '/opt/freesurfer/subjects'} graymid = in_file = /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003126-fmriprep/sourcedata/freesurfer/sub-047EPKL012074/surf/lh.smoothwm nsurfaces = out_name = midthickness pial = smooth_averages = sphere = sphere spring = subjects_dir = /opt/freesurfer/subjects thickness = True thickness_name = write_iterations =

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 _midthickness0.

RuntimeError: subprocess exited with code 134. ...skipping... Node: _midthickness0 Working directory: /scratch1/03201/jbwexler/work_dir/fmriprep/ds003126_sub-047EPKL012074/fmriprep_22_0_wf/single_subject_047EPKL012074_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0

Node inputs:

args = distance = 0.5 dt = environ = {'SUBJECTS_DIR': '/opt/freesurfer/subjects'} graymid = in_file = /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds003126-fmriprep/sourcedata/freesurfer/sub-047EPKL012074/surf/lh.smoothwm nsurfaces = out_name = midthickness pial = smooth_averages = sphere = sphere spring = subjects_dir = /opt/freesurfer/subjects thickness = True thickness_name = write_iterations =

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 _midthickness0.

RuntimeError: subprocess exited with code 134.

effigies commented 1 year ago

Seems to be https://github.com/nipreps/smriprep/issues/294. We didn't really track that down, but looks like a good one to debug manually.