When running both recon-all within C-PAC via Nipype and the ABCD surface post-processing workflow, the pipeline tends to hang roughly around the timeseries warp-to-template part of the pipeline, although the warp-to-template portion seems unrelated to the stall (which really confounded the debugging efforts).
This most notably impacts the abcd-options preconfig and/or the options commonly associated with it.
This error will not happen if:
recon-all is run outside of C-PAC first, then the results ingressed into C-PAC and surface post-processing run afterwards.
If recon-all is run inside C-PAC but surface post-processing is not enabled.
If this error occurs, it can also be bypassed by:
Cancelling the stalled pipeline, and then re-starting it as-is via warm restart (if the Nipype working directory remains).
I suspect it is the combination of recon-all and its outputs' Nipype pointer connections to the surface post-processing nodes, in some way. Fortunately, we are moving away from recon-all being run within C-PAC in the near future.
To reproduce
Simply run the abcd-options preconfig with recon-all enabled within C-PAC, instead of ingressing Freesurfer results from a previous Freesurfer run.
Preconfig
[ ] default
[X] abcd-options
[ ] anat-only
[ ] blank
[ ] ccs-options
[ ] fmriprep-options
[ ] fx-options
[ ] monkey
[ ] monkey-ABCD
[ ] ndmg
[ ] nhp-macaque
[ ] preproc
[ ] rbc-options
[ ] rodent
Custom pipeline configuration
No response
Run command
No response
Expected behavior
The pipeline should simply complete.
Acceptance criteria
[ ] An abcd-options pipeline run with Freesurfer recon-all run as part of the pipeline, and then the pipeline completes successfully with no intervention.
Describe the bug
When running both
recon-allwithin C-PAC via Nipype and the ABCD surface post-processing workflow, the pipeline tends to hang roughly around the timeseries warp-to-template part of the pipeline, although the warp-to-template portion seems unrelated to the stall (which really confounded the debugging efforts).This most notably impacts the
abcd-optionspreconfig and/or the options commonly associated with it.This error will not happen if:
recon-allis run outside of C-PAC first, then the results ingressed into C-PAC and surface post-processing run afterwards.recon-allis run inside C-PAC but surface post-processing is not enabled.If this error occurs, it can also be bypassed by:
I suspect it is the combination of
recon-alland its outputs' Nipype pointer connections to the surface post-processing nodes, in some way. Fortunately, we are moving away fromrecon-allbeing run within C-PAC in the near future.To reproduce
abcd-optionspreconfig withrecon-allenabled within C-PAC, instead of ingressing Freesurfer results from a previous Freesurfer run.Preconfig
Custom pipeline configuration
No response
Run command
No response
Expected behavior
The pipeline should simply complete.
Acceptance criteria
abcd-optionspipeline run with Freesurferrecon-allrun as part of the pipeline, and then the pipeline completes successfully with no intervention.Screenshots
No response
C-PAC version
v1.8.7
Container platform
No response
Docker and/or Singularity version(s)
No response
Additional context
No response