ds002185-mriqc: Segmentation fault

[jbwexler]

Only for two subjects. Rerunning didn't solve it.

Traceback (most recent call last): File "/opt/conda/bin/mriqc", line 8, in sys.exit(main()) File "/opt/conda/lib/python3.8/site-packages/mriqc/cli/run.py", line 158, in main mriqc_wf.run(**_plugin) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/workflows.py", line 632, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/opt/conda/lib/python3.8/site-packages/mriqc/engine/plugin.py", line 184, in run self._clean_queue(jobid, graph, result=result) File "/opt/conda/lib/python3.8/site-packages/mriqc/engine/plugin.py", line 256, in _clean_queue raise RuntimeError("".join(result["traceback"])) RuntimeError: Traceback (most recent call last): File "/opt/conda/lib/python3.8/site-packages/mriqc/engine/plugin.py", line 60, 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_in terface return self._run_command(execute) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_co mmand result = self._interface.run(cwd=outdir) File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 419, in run runtime = self._run_interface(runtime) File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/fsl/preprocess.py", line 164, in _ru n_interface self.raise_exception(runtime) File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 741, in raise_ex ception raise RuntimeError( RuntimeError: Command: bet /scratch1/03201/jbwexler/work_dir/mriqc/ds002185_sub-14/mriqc_wf/anatMRIQC/synthstrip_wf/_infile ..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds002185-mriqc..sourcedata.. raw..sub-14..anat..sub-14_acq-space_T2w.nii.gz/post_n4/clipped_corrected.nii.gz /scratch1/03201/jbwex ler/work_dir/mriqc/ds002185_sub-14/mriqc_wf/anatMRIQC/HeadMaskWorkflow/_infile..scratch1..03201..jb wexler..openneuro_derivatives..derivatives..mriqc..ds002185-mriqc..sourcedata..raw..sub-14..anat..sub-14_acq-space_T2w.nii.gz/fsl_bet/clipped_corrected_brain.nii.gz -A Standard output:

Standard error: Segmentation fault Return code: 0

(END)

[jbwexler]

Recently got a similar error for all subjects in ds003823:

Traceback (most recent call last): File "/opt/conda/bin/mriqc", line 8, in sys.exit(main()) File "/opt/conda/lib/python3.9/site-packages/mriqc/cli/run.py", line 167, in main mriqc_wf.run(**_plugin) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/opt/conda/lib/python3.9/site-packages/mriqc/engine/plugin.py", line 184, in run self._clean_queue(jobid, graph, result=result) File "/opt/conda/lib/python3.9/site-packages/mriqc/engine/plugin.py", line 256, in _clean_queue raise RuntimeError("".join(result["traceback"])) RuntimeError: Traceback (most recent call last): File "/opt/conda/lib/python3.9/site-packages/mriqc/engine/plugin.py", line 60, 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 fsl_bet.

Cmdline: bet clipped_corrected.nii.gz clipped_corrected_brain.nii.gz -A Stdout:

Stderr: Segmentation fault Traceback: 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 clipped_corrected.nii.gz clipped_corrected_brain.nii.gz -A Standard output:

    Standard error:
    Segmentation fault
    Return code: 0

[effigies]

I would look at the files that it failed on, e.g. /scratch1/03201/jbwexler/work_dir/mriqc/ds002185_sub-14/mriqc_wf/anatMRIQC/synthstrip_wf/_in_file _..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds002185-mriqc..sourcedata.. raw..sub-14..anat..sub-14_acq-space_T2w.nii.gz/post_n4/clipped_corrected.nii.gz. Doesn't look like it's still on TACC. If there's nothing visually wrong with it, I'd try running BET on it locally.

[jbwexler]

Looks like the issue here is due to some anatomical files having a small fov: https://openneuro.org/datasets/ds003823/versions/1.3.3/file-display/sub-5001:ses-post:anat:sub-5001_ses-post_acq-lc_T1w.nii.gz

Is there a way to deal with that in mriqc? Or just ignore them?