fMRIPrep crashes on singularity

Hi all,

I know it’s a bit basic, I’m running fMRIPrep 20.2.6 on a cluster via singularity (image created by:

singularity build /my_images/fmriprep-20-2-6.simg docker://nipreps/fmriprep:20.2.6

)

and I’m getting the following crash (from log file)

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 521, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 639, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 751, in _run_command
    f"Exception raised while executing Node {self.name}.\n\n{result.runtime.traceback}"
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node _parcstats1.

RuntimeError: subprocess exited with code 1.

From the stdout it looks:

220110-05:11:53,310 nipype.interface INFO:
         resume recon-all : recon-all -autorecon-hemi rh -nohyporelabel -openmp 8 -subjid sub-AlZi -sd /data/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
220110-05:13:26,887 nipype.workflow INFO:
         [Node] Finished "_parcstats1", elapsed time 93.577859s.
220110-05:13:26,904 nipype.workflow WARNING:
         [Node] Error on "_parcstats1" (/sci/home/uri.elias/work/fmriprep_wf/single_subject_SBJ1_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats1)
220110-05:13:28,360 nipype.workflow ERROR:
         Node _parcstats1 failed to run on host glacier-37.
220110-05:13:28,384 nipype.workflow ERROR:
         Saving crash info to /data/fmriprep/sub-SBJ1/log/20220109-205515_e7e08e3d-d956-458a-b890-ded5e70a5820/crash-20220110-051328-uri.elias-_parcstats1-8e589e10-a7f8-4b99-8f08-bc5d6950f3ee.txt
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 521, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 639, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 751, in _run_command
    f"Exception raised while executing Node {self.name}.\n\n{result.runtime.traceback}"
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node _parcstats1.

RuntimeError: subprocess exited with code 1.

220110-05:16:04,451 nipype.workflow INFO:
         [Node] Finished "_parcstats0", elapsed time 251.803173s.
220110-05:16:08,471 nipype.workflow ERROR:
         could not run node: fmriprep_wf.single_subject_SBJ1_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.parcstats
220110-05:16:09,244 nipype.workflow CRITICAL:
         fMRIPrep failed: Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 521, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 639, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 751, in _run_command
    f"Exception raised while executing Node {self.name}.\n\n{result.runtime.traceback}"
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node _parcstats1.

RuntimeError: subprocess exited with code 1.

Where can I start understanding what’s wrong?
Thanks!

For FreeSurfer errors, please check the FreeSurfer logs. Since this was a RH job, you’ll want sub-AlZi/scripts/recon-all-rh.log.

Thanks! you’re a genius:) it worked!! (apparently the fsaverage dir was only half filled from previous runs. Removing and rerunning solved the issue)

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