🐛 Freesurfer-based pipeline options cause a hang in a specific use case

[sgiavasis]

Describe the bug

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

1. 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
• 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.

Screenshots

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C-PAC version

v1.8.7

Container platform

No response

Docker and/or Singularity version(s)

No response

Additional context

No response