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Freesurfer-based pipeline hangs if recon-all and ABCD surface post-processing are run in the same pipeline¶

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See issue #2104 for the latest developments on this issue.

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When running both recon-all within C-PAC via Nipype and the ABCD surface post-processing workflow,

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# PREPROCESSING
+# -------------
+surface_analysis:
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+  # Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives.
+  # If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
+  # select those 'Freesurfer-' labeled options further below in anatomical_preproc.
+  freesurfer:
+    run_reconall: On
+
+  # Run ABCD-HCP post FreeSurfer and fMRISurface pipeline
+  post_freesurfer:
+    run: On
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+
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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.

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(The stall always happens with one of the abcd timeseries warp-to-template nodeblock’s nodes being listed in the pypeline.log as the last to complete - and when you search the working directory, often ANTs registration never even started.)

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However, post-proc runs well on its own. It’s the combination.

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Workarounds¶

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Preferred¶

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Running FreeSurfer recon-all first and ingressing its outputs, which is now our recommended usage, doesn’t hit this problem.

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Alternative¶

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Running it normally, hitting a stall, and simply restarting the pipeline run also gets past it. That is, cancelling the stalled pipeline, and then re-starting it as-is via warm restart (if the Nipype working directory remains).

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Planned resolution¶

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  • Removing FreeSurfer recon-all as a workflow within C-PAC, instead requiring its outputs as input data for configurations that involve surface analysis.

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