🥅 Add registration guardrails

[shnizzedy]

Fixes

Related to FCP-INDI/TheWay#8 by @shnizzedy

Description

QC checks registration steps and either crashes or changes the random seed and retries the step.

Thresholds are specified in the pipeline config

C-PAC/CPAC/resources/configs/pipeline_config_default.yml

Lines 587 to 597 in b9a7ad0

	registration_workflows:
	# Minimum QC values to allow a run to complete post-registration
	# Set any metric empty (like "Dice:") or to None to disable that guardrail
	# Default thresholds adopted from XCP-Engine
	# (https://github.com/PennLINC/xcpEngine/blob/397ab6cf/designs/cbf_all.dsn#L66)
	quality_thresholds:
	Dice: 0.8
	Jaccard: 0.9
	CrossCorr: 0.7
	Coverage: 0.8

Technical details

Guardrails strategy

For a node that calculates a warp:

1. Make a clone with an incremented seed.
2. Put a guardrail on each of those two nodes, with the retry node raising a BadRegistrationError on QC failure.
3. For each output, use a sequence of Nipype Merge and Select utility nodes to choose which node's outputs to used based on the failure status of the first-try node's guardrail.
   

I've got some (I think) good ideas to abstract the guardrails further so the installation can be simpler in the future, but that'll be after 1.8.5 (if ever).

Also

• Changes random.log with a single logged seed to random.tsv with a logged seed per try (to record the incremented seed for any retries that succeed where the first try failed)
• Adds fallback forkable option for BBR where
  • Off does no BBR;
  • On does one BBR attempt with one seed-incremented retry;
  • fallback does one BBR attempt, falling back to no-BBR on failure
• Exposes Nipype's stop_on_first_crash configuration option with new fail_fast config option

Checklist

• My pull request has a descriptive title (not a vague title like Update index.md).
• My pull request targets the develop branch of the repository.
• My commit messages follow best practices.
• My code follows the established code style of the repository.
• I added tests for the changes I made (if applicable).
• I updated the changelog.
• I added or updated documentation (📝 Document registration guardrails fcp-indi.github.io#293, in progress).
• I tried running the project locally and verified that there are no visible errors.

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[shnizzedy]

@FCP-INDI/developers I'll do the merge conflict resolution on Monday, but in reviewing this, please particularly look to see if I put the guardrails in appropriate places (where needed, not where not needed).