Summary of what happened:
I’m running brains from this dataset, OpenNeuro, through fmriprep. I get the same error with each brain
Exception raised while executing Node _parcstats0.
Command used (and if a helper script was used, a link to the helper script or the command generated):
singularity run --cleanenv --bind ${BIDS_DIR} --bind ${OUT_DIR} --bind ${WORK_DIR} ${SINGULARITY_IMAGE} ${BIDS_DIR} ${OUT_DIR} participant --participant_label $ppt -w ${WORK_DIR} --use-syn-sdc --output-spaces MNI152NLin6Asym MNI152NLin2009cAsym fsLR fsaverage --cifti-output --stop-on-first-crash --fs-license-file ~sapskr/license.txt
(works successfully with other datasets)
Version:
24.0.0
Environment (Docker, Singularity / Apptainer, custom installation):
Docker
Data formatted according to a validatable standard? Please provide the output of the validator:
bids-validator@1.14.6
e[32mThis dataset appears to be BIDS compatible.e[39m
e[34me[4mSummary:e[24me[39m e[34me[4mAvailable Tasks:e[24me[39m e[34me[4mAvailable Modalities:e[39me[24m
110 Files, 3.47GB movie MRI
26 - Subjects
1 - Session
Relevant log outputs (up to 20 lines):
[Node] Setting-up "_parcstats0" in "/cubric/scratch/sapskr/CUBIC_dance/work/fmriprep_24_0_wf/sub_25_wf/anat_fit_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats0".
240906-17:19:11,787 nipype.workflow INFO:
[Node] Executing "_parcstats0" <smriprep.interfaces.freesurfer.ReconAll>
240906-17:19:11,791 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi lh -nohyporelabel -lh-only -openmp 8 -subjid sub-25 -sd /cubric/scratch/sapskr/CUBIC_dance/derivatives/sourcedata/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
240906-17:19:11,792 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi lh -nohyporelabel -lh-only -openmp 8 -subjid sub-25 -sd /cubric/scratch/sapskr/CUBIC_dance/derivatives/sourcedata/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
240906-17:20:28,260 nipype.workflow INFO:
[Node] Finished "_parcstats0", elapsed time 76.472014s.
240906-17:20:28,268 nipype.workflow WARNING:
[Node] Error on "_parcstats0" (/cubric/scratch/sapskr/CUBIC_dance/work/fmriprep_24_0_wf/sub_25_wf/anat_fit_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats0)
240906-17:20:29,48 nipype.workflow ERROR:
Node _parcstats0 failed to run on host c4b10.
240906-17:20:29,56 nipype.workflow ERROR:
Saving crash info to /cubric/scratch/sapskr/CUBIC_dance/derivatives/sub-25/log/20240906-120332_b98d39bd-7bf2-4486-9396-0d2e8e8d1e09/crash-20240906-172029-sapskr-_parcstats0-8e5072e6-949f-4282-badd-5673cd27d4de.txt
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/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 _parcstats0.
Cmdline:
recon-all -autorecon-hemi lh -nohyporelabel -lh-only -openmp 8 -subjid sub-25 -sd /cubric/scratch/sapskr/CUBIC_dance/derivatives/sourcedata/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
Stdout:
fs-check-version --s sub-25 --o /tmp/tmp.cIBJRi
Fri Sep 6 17:19:12 BST 2024