🥅 Add registration guardrails #1814

shnizzedy · 2022-10-31T14:24:31Z

Fixes

Recreation of #1789 by @shnizzedy
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:

Make a clone with an incremented seed.
Put a guardrail on each of those two nodes, with the retry node raising a BadRegistrationError on QC failure.
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
🔧 Add fail_fast to expose Nipype's stop_on_first_crash #1816

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.

Developer Certificate of Origin

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(a) The contribution was created in whole or in part by me and I
    have the right to submit it under the open source license
    indicated in the file; or

(b) The contribution is based upon previous work that, to the best
    of my knowledge, is covered under an appropriate open source
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    by me, under the same open source license (unless I am
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…nfig

[skip ci]

Co-authored-by: Steve Giavasis <sgiava77@gmail.com>

…ging seed Co-authored-by: Mike Milham <Michael.Milham@childmind.org> Co-authored-by: Steve Giavasis <sgiava77@gmail.com>

Squashed commit of the following: commit 356dc30 Merge: b1ce64b 55667a2 Author: Steve Giavasis <sgiava77@gmail.com> Date: Fri Oct 14 16:33:28 2022 -0400 Merge pull request #1778 from FCP-INDI/deeper-config-path 🚚 Move C-PAC generated configs into `log/sub-${sub}_ses-${ses}` subdirectory commit b1ce64b Merge: 37a6874 c6ec0a0 Author: Steve Giavasis <sgiava77@gmail.com> Date: Fri Oct 14 16:33:19 2022 -0400 Merge pull request #1769 from FCP-INDI/feature/total_readout_time Ingress and use TotalReadoutTime from epi fmap meta-data in FSL topup commit c6ec0a0 Merge: 8301e3c 37a6874 Author: Steve Giavasis <sgiava77@gmail.com> Date: Fri Oct 14 16:03:28 2022 -0400 Merge branch 'develop' into feature/total_readout_time commit 8301e3c Author: Steve Giavasis <sgiava77@gmail.com> Date: Fri Oct 14 15:56:44 2022 -0400 Revert to using dwell time first to maintain original DCAN script's functionality commit 55667a2 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Oct 14 15:55:55 2022 -0400 :art: Include minimized pipeline config in hardlinking step commit a641d00 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Oct 14 15:44:42 2022 -0400 :lock: Make generated config files read-only Co-authored-by: Steve Giavasis <sgiava77@gmail.com> commit 37a6874 Merge: b5d0d1f 5b2465f Author: Steve Giavasis <sgiava77@gmail.com> Date: Fri Oct 14 15:46:39 2022 -0400 Merge pull request #1787 from diegoaper/main 🐛 ✅ Group Runner 1.8 and MDMR Changes commit cb5bc42 Merge: 9c0a89c b5d0d1f Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Oct 14 15:37:53 2022 -0400 :twisted_rightwards_arrows: Merge develop into deeper-config-path commit b5d0d1f Merge: 7f50838 dc3f113 Author: Steve Giavasis <sgiava77@gmail.com> Date: Fri Oct 14 15:19:13 2022 -0400 Merge pull request #1796 from clane9/bugfix/random_seed 🐛 fix type handling in `set_up_random_state` commit dc3f113 Merge: 0ccc40d 7f50838 Author: Steve Giavasis <sgiava77@gmail.com> Date: Fri Oct 14 15:18:31 2022 -0400 Merge branch 'develop' into bugfix/random_seed commit 7f50838 Merge: 8ebf0a7 c2ba9d6 Author: Steve Giavasis <sgiava77@gmail.com> Date: Fri Oct 14 15:17:39 2022 -0400 Merge pull request #1790 from FCP-INDI/backwards-compatibility/default_pipeline.yml ⚰️ Add placeholder default_pipeline.yml for backwards compatibility commit 8ebf0a7 Merge: fd91a42 0182f98 Author: Steve Giavasis <sgiava77@gmail.com> Date: Fri Oct 14 15:16:59 2022 -0400 Merge pull request #1788 from FCP-INDI/rbc-update 🔧 Base `rbc-options` on `fmriprep-options`' preproc commit fd91a42 Merge: 6b402b0 76a4a75 Author: Steve Giavasis <sgiava77@gmail.com> Date: Fri Oct 14 15:16:14 2022 -0400 Merge pull request #1781 from FCP-INDI/fix/FUGUE--dwell 🐛 Fix `FUGUE --dwell` parameterization commit 0ccc40d Author: Connor Lane <connor.lane858@gmail.com> Date: Thu Oct 13 16:55:12 2022 -0400 move changelog entry to the unreleased section commit b5c742a Author: Connor Lane <connor.lane858@gmail.com> Date: Wed Oct 12 17:43:26 2022 -0400 update changelog commit 6b402b0 Author: Jon Clucas <jon.clucas@childmind.org> Date: Wed Oct 12 16:12:59 2022 -0400 fixup! :fast_forward: Bring `develop` up to date with `main` commit 5867210 Author: Connor Lane <connor.lane858@gmail.com> Date: Wed Oct 12 09:48:39 2022 -0400 :bug: fix type handling in `set_up_random_state` commit 5b2465f Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Tue Oct 11 11:48:57 2022 -0400 Removed participant Configuration commit 92f9658 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Mon Oct 10 14:09:46 2022 -0400 Update cpac_group_runner.py commit a112d34 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Mon Oct 10 10:40:56 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 031946a Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Mon Oct 10 10:40:35 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit df2bb33 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Mon Oct 10 10:40:00 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit c5d306d Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Mon Oct 10 10:39:46 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit e903b98 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Mon Oct 10 10:39:16 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 82e2ece Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Mon Oct 10 10:38:50 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit d75dbe3 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Mon Oct 10 10:38:32 2022 -0400 Update 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<jon.clucas@childmind.org> commit 6fcb279 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:22:10 2022 -0400 Update CPAC/cwas/cwas.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit f25b604 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:22:04 2022 -0400 Update CPAC/cwas/cwas.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 35318a5 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:21:52 2022 -0400 Update CPAC/cwas/cwas.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 6ccce46 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:20:28 2022 -0400 Update CPAC/cwas/cwas.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 6dc4a2b Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 10:55:53 2022 -0400 Update cpac_outputs.tsv Added 2 lines for MDMR group_analysis output commit b6ed208 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 10:48:47 2022 -0400 Update group_config_template.yml commit 2ab1d64 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 10:48:09 2022 -0400 Fixed 1.8.4 image intake Fixed the intake for images to make the 1.8.4 BIDS convention. commit 68e3416 Merge: 32632fa 9586d71 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Oct 7 10:20:22 2022 -0400 :fast_forward: Bring `develop` up to date with `main` commit c2ba9d6 Author: Jon Clucas <jon.clucas@childmind.org> Date: Wed Oct 5 15:16:39 2022 -0400 :coffin: Add placeholder default_pipeline.yml for backwards compatibility [skip ci] commit 76a4a75 Author: Jon Clucas <jon.clucas@childmind.org> Date: Wed Oct 5 17:51:41 2022 +0000 :recycle: Send 'desc-mean_bold' as input to `distcor_blip_fsl_topup` Co-authored-by: Steve Giavasis <sgiava77@gmail.com> commit 0182f98 Author: Jon Clucas <jon.clucas@childmind.org> Date: Wed Oct 5 11:12:03 2022 -0400 :memo: Add rbc-options update to CHANGELOG [skip ci] Co-authored-by: Greg Kiar <gkiar@users.noreply.github.com> commit 5208944 Author: Jon Clucas <jon.clucas@childmind.org> Date: Tue Oct 4 17:00:49 2022 -0400 :wrench: Base rbc-options on fmriprep-options Co-authored-by: Greg Kiar <gkiar@users.noreply.github.com> commit 1ab4086 Author: Jon Clucas <jon.clucas@childmind.org> Date: Tue Oct 4 20:48:57 2022 +0000 :recycle: Replumb to prevent wild TOPUP forking Co-authored-by: Steve Giavasis <sgiava77@gmail.com> commit c3ac6ac Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Tue Oct 4 15:48:30 2022 -0400 MDMR Group Config Template Update to the scripts and config template commit eee5461 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 30 21:21:15 2022 +0000 :recycle: Fix cyclical imports commit db27851 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 30 16:37:46 2022 -0400 :alien: Import typehints in function node commit c148153 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 30 15:41:34 2022 +0000 :loud_sound: Add FSL-`DwellTime` fix to CHANGELOG [skip ci] Co-authored-by: Nathalia Esper <nathbianchini@gmail.com> Co-authored-by: Alex Franco <eng.franco@gmail.com> commit e53581b Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 30 15:27:52 2022 +0000 :bug: Fix import path commit 2338585 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 30 15:24:38 2022 +0000 :page_facing_up: Add/update LGPL-3-or-later notice to modified files [skip ci] commit 109d536 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 30 15:11:39 2022 +0000 :recycle: Only look for `EffectiveEchoSpacing` in functional sidecar commit 695d29a Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 30 14:41:04 2022 +0000 :rotating_light: Remove duplicate good-name [skip ci] commit c9bea18 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 30 14:37:12 2022 +0000 :recycle: DRY and let `calc_delta_te_and_asym_ratio` determine EES source commit 55ca4d9 Author: Jon Clucas <jon.clucas@childmind.org> Date: Thu Sep 29 14:09:12 2022 +0000 :bug: Fix logic checking for `diffphase-effectiveEchoSpacing` commit d41dc29 Author: Jon Clucas <jon.clucas@childmind.org> Date: Wed Sep 28 12:42:26 2022 -0400 :bug: Only connect calc_delta_ratio if diff commit ca86b0b Author: Jon Clucas <jon.clucas@childmind.org> Date: Wed Sep 28 09:56:32 2022 -0400 :bug: Fix plumbing for EffectiveEchoSpacing commit f7ca070 Author: Jon Clucas <jon.clucas@childmind.org> Date: Tue Sep 27 17:26:49 2022 -0400 :recycle: Get EffectiveEchoSpacing from func metadata if possible commit 376d550 Author: Jon Clucas <jon.clucas@childmind.org> Date: Tue Sep 27 15:19:59 2022 -0400 :bug: Update DwellTime → EffectiveEchoSpacing for FSL FUGUE Co-authored-by: Nathalia Esper <nathbianchini@gmail.com> Co-authored-by: Alex Franco <eng.franco@gmail.com> commit 32632fa Merge: eed40c5 238f499 Author: Steve Giavasis <sgiava77@gmail.com> Date: Mon Sep 26 13:23:08 2022 -0400 Merge pull request #1777 from FCP-INDI/differentiate-sametime-data-configs 🐛 Differentiate sametime data and pipeline configs commit eed40c5 Merge: 76eb34d a64541e Author: Steve Giavasis <sgiava77@gmail.com> Date: Mon Sep 26 13:22:50 2022 -0400 Merge pull request #1775 from FCP-INDI/deeper-working-path 🚚 Use `f'pipeline_{pipeline_name}'` subdirectories for `log`, `working`, and `output` commit 76eb34d Author: sgiavasis <sgiava77@gmail.com> Date: Mon Sep 26 17:21:02 2022 +0000 Merge resolution for latest nuisance and native/template-space options changes. commit b30a2e0 Merge: 1e24c69 ea18242 Author: sgiavasis <sgiava77@gmail.com> Date: Sun Sep 25 08:30:26 2022 +0000 Merge branch 'dev-fix' into develop commit ea18242 Author: sgiavasis <sgiava77@gmail.com> Date: Sun Sep 25 08:27:49 2022 +0000 Staging changes from template-space derivatives for next release. commit 9c0a89c Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 23 12:48:29 2022 -0400 :bug: Create nested working directory before writing PID to disk commit d50f8da Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 23 12:26:11 2022 -0400 :recycle: Move PID on disk one level deeper in working directory commit 137c482 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 23 12:17:07 2022 -0400 :recycle: Modularize checking p_name commit 1899c9e Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 23 10:50:41 2022 -0400 :truck: Nest `failedToStart.log` as deeply as possible commit ed554a6 Merge: 0490394 a64541e Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 23 10:33:30 2022 -0400 :twisted_rightwards_arrow: Merge develop into deeper-config-path commit 238f499 Merge: 68ac96a 1e24c69 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 23 10:19:13 2022 -0400 :twisted_rightwards_arrows: Merge develop into differentiate-sametime-data-configs commit a64541e Merge: e5ec37c 1e24c69 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 23 10:14:02 2022 -0400 :twisted_rightwards_arrows: Merge develop into deeper-working-path commit 0490394 Author: Jon Clucas <jon.clucas@childmind.org> Date: Thu Sep 22 14:38:02 2022 -0400 :pencil2: Set c['subject_id'] commit f3aefca Author: Jon Clucas <jon.clucas@childmind.org> Date: Thu Sep 22 12:20:57 2022 -0400 :truck: Move C-PAC-generated data and pipeline configs one level deeper commit 2ed4d6a Author: Jon Clucas <jon.clucas@childmind.org> Date: Thu Sep 22 11:21:48 2022 -0400 :truck: Move C-PAC-generated config files into log dir commit 19c3890 Merge: e5ec37c 68ac96a Author: Jon Clucas <jon.clucas@childmind.org> Date: Thu Sep 22 10:59:04 2022 -0400 :twisted_rightwards_arrows: Merge differentiate-sametime-data-configs into deeper-config-path commit 68ac96a Author: Jon Clucas <jon.clucas@childmind.org> Date: Wed Sep 21 17:37:02 2022 -0400 :white_check_mark: Add unit test for hash_data_config commit 6003194 Author: Jon Clucas <jon.clucas@childmind.org> Date: Wed Sep 21 17:07:57 2022 -0400 :loud_sound: Add config hash string update to CHANGELOG commit e5ec37c Merge: e09cfa0 14e1591 Author: Jon Clucas <jon.clucas@childmind.org> Date: Wed Sep 21 16:36:39 2022 -0400 :twisted_rightwards_arrows: Merge develop into deeper-working-path commit e09cfa0 Author: Jon Clucas <jon.clucas@childmind.org> Date: Wed Sep 21 16:13:35 2022 -0400 :bug: Change working path update location commit 9586d71 Merge: 12c4f74 94d8082 Author: Steve Giavasis <sgiava77@gmail.com> Date: Mon Sep 19 21:31:01 2022 -0400 Merge pull request #1764 from FCP-INDI/fix/pipeline-config-versions 🔖 Hotfix: Update version to 1.8.4 commit 94d8082 Author: sgiavasis <sgiava77@gmail.com> Date: Tue Sep 20 01:27:46 2022 +0000 Fix Neurostars link in the README. commit 8804f61 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 16 15:23:00 2022 -0400 :art: Rename `f'cpac_{pipeline_name}'` directories to `f'pipeline_{pipeline_name}'` to match `output`, `log`, and `working` subdirectories Co-authored-by: Steve Giavasis <sgiava77@gmail.com> commit 77a1c5c Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 16 15:13:12 2022 -0400 :truck: Add pipeline-config-level directory for participant working directories commit 7718419 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 16 14:49:31 2022 -0400 :goal_net: Sanitize `pipeline_name` during validation commit ce6dd09 Author: sgiavasis <sgiava77@gmail.com> Date: Fri Sep 9 18:51:27 2022 +0000 Updated changelog. commit 7f42613 Author: sgiavasis <sgiava77@gmail.com> Date: Fri Sep 9 18:45:47 2022 +0000 Improved the error message for missing epi field map meta-data. commit d43aa6c Author: sgiavasis <sgiava77@gmail.com> Date: Fri Sep 9 04:14:31 2022 +0000 Read in TotalReadoutTime from field map metadata, if it exists. Pass TotalReadoutTime to FSL TOPUP if present. commit 9453398 Author: Theodore (Machine User) <CMI_CPAC_Support@childmind.org> Date: Wed Aug 31 17:42:23 2022 +0000 :bookmark: Update version to 1.8.4 (:construction_worker: Differentiate between Git branches and tags for Docker tags)

[skip ci]

Squashed commit of the following: commit ba782c1 Author: Jon Clucas <jon.clucas@childmind.org> Date: Tue Oct 18 14:36:38 2022 -0400 :truck: Include graph2use in graph filenames commit b132f10 Author: Jon Clucas <jon.clucas@childmind.org> Date: Tue Oct 18 12:32:44 2022 -0400 :wrench: Add graphviz options to pipeline config commit a72f1a6 Author: Jon Clucas <jon.clucas@childmind.org> Date: Mon Oct 17 17:25:27 2022 -0400 :art: Update dotgraph building to quote strings (to allow `-`s) commit 356dc30 Merge: b1ce64b 55667a2 Author: Steve Giavasis <sgiava77@gmail.com> Date: Fri Oct 14 16:33:28 2022 -0400 Merge pull request #1778 from FCP-INDI/deeper-config-path 🚚 Move C-PAC generated configs into `log/sub-${sub}_ses-${ses}` subdirectory commit b1ce64b Merge: 37a6874 c6ec0a0 Author: Steve Giavasis <sgiava77@gmail.com> Date: Fri Oct 14 16:33:19 2022 -0400 Merge pull request #1769 from FCP-INDI/feature/total_readout_time Ingress and use TotalReadoutTime from epi fmap meta-data in FSL topup commit c6ec0a0 Merge: 8301e3c 37a6874 Author: Steve Giavasis <sgiava77@gmail.com> Date: Fri Oct 14 16:03:28 2022 -0400 Merge branch 'develop' into feature/total_readout_time commit 8301e3c Author: Steve Giavasis <sgiava77@gmail.com> Date: Fri Oct 14 15:56:44 2022 -0400 Revert to using dwell time first to maintain original DCAN script's functionality commit 55667a2 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Oct 14 15:55:55 2022 -0400 :art: Include minimized pipeline config in hardlinking step commit a641d00 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Oct 14 15:44:42 2022 -0400 :lock: Make generated config files read-only Co-authored-by: Steve Giavasis <sgiava77@gmail.com> commit 37a6874 Merge: b5d0d1f 5b2465f Author: Steve Giavasis <sgiava77@gmail.com> Date: Fri Oct 14 15:46:39 2022 -0400 Merge pull request #1787 from diegoaper/main 🐛 ✅ Group Runner 1.8 and MDMR Changes commit cb5bc42 Merge: 9c0a89c b5d0d1f Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Oct 14 15:37:53 2022 -0400 :twisted_rightwards_arrows: Merge develop into deeper-config-path commit b5d0d1f Merge: 7f50838 dc3f113 Author: Steve Giavasis <sgiava77@gmail.com> Date: Fri Oct 14 15:19:13 2022 -0400 Merge pull request #1796 from clane9/bugfix/random_seed 🐛 fix type handling in `set_up_random_state` commit dc3f113 Merge: 0ccc40d 7f50838 Author: Steve Giavasis <sgiava77@gmail.com> Date: Fri Oct 14 15:18:31 2022 -0400 Merge branch 'develop' into bugfix/random_seed commit 7f50838 Merge: 8ebf0a7 c2ba9d6 Author: Steve Giavasis <sgiava77@gmail.com> Date: Fri Oct 14 15:17:39 2022 -0400 Merge pull request #1790 from FCP-INDI/backwards-compatibility/default_pipeline.yml ⚰️ Add placeholder default_pipeline.yml for backwards compatibility commit 8ebf0a7 Merge: fd91a42 0182f98 Author: Steve Giavasis <sgiava77@gmail.com> Date: Fri Oct 14 15:16:59 2022 -0400 Merge pull request #1788 from FCP-INDI/rbc-update 🔧 Base `rbc-options` on `fmriprep-options`' preproc commit fd91a42 Merge: 6b402b0 76a4a75 Author: Steve Giavasis <sgiava77@gmail.com> Date: Fri Oct 14 15:16:14 2022 -0400 Merge pull request #1781 from FCP-INDI/fix/FUGUE--dwell 🐛 Fix `FUGUE --dwell` parameterization commit 0ccc40d Author: Connor Lane <connor.lane858@gmail.com> Date: Thu Oct 13 16:55:12 2022 -0400 move changelog entry to the unreleased section commit b5c742a Author: Connor Lane <connor.lane858@gmail.com> Date: Wed Oct 12 17:43:26 2022 -0400 update changelog commit 6b402b0 Author: Jon Clucas <jon.clucas@childmind.org> Date: Wed Oct 12 16:12:59 2022 -0400 fixup! :fast_forward: Bring `develop` up to date with `main` commit 5867210 Author: Connor Lane <connor.lane858@gmail.com> Date: Wed Oct 12 09:48:39 2022 -0400 :bug: fix type handling in `set_up_random_state` commit 5b2465f Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Tue Oct 11 11:48:57 2022 -0400 Removed participant Configuration commit 92f9658 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Mon Oct 10 14:09:46 2022 -0400 Update cpac_group_runner.py commit a112d34 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Mon Oct 10 10:40:56 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 031946a Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Mon Oct 10 10:40:35 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit df2bb33 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Mon Oct 10 10:40:00 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit c5d306d Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Mon Oct 10 10:39:46 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit e903b98 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Mon Oct 10 10:39:16 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 82e2ece Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Mon Oct 10 10:38:50 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit d75dbe3 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Mon Oct 10 10:38:32 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 9407c63 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Mon Oct 10 10:38:11 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 61097e3 Merge: 0ba271a 750c9ec Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Mon Oct 10 10:37:40 2022 -0400 Merge branch 'main' of https://github.com/diegoaper/C-PAC_MDMR-Group_Runner commit 0ba271a Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Mon Oct 10 10:37:29 2022 -0400 Update cpac_group_runner.py commit 750c9ec Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Mon Oct 10 10:37:04 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit cf81d08 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:36:52 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit e570fbf Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:36:38 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 2eea1f4 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:35:59 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 99620c6 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:35:44 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit cf8f0d9 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:33:11 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit de6235f Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:32:40 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit ebe6a27 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:32:26 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit c50db8d Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:30:13 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 748f376 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:29:26 2022 -0400 Update CPAC/cwas/pipeline.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 6d938f4 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:28:55 2022 -0400 Update CPAC/cwas/pipeline.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 0b2b868 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:28:20 2022 -0400 Update CPAC/cwas/pipeline.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 281427d Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:27:24 2022 -0400 Update CPAC/cwas/cwas.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 63c3ad4 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:27:15 2022 -0400 Update CPAC/cwas/cwas.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit ca75679 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:27:05 2022 -0400 Update CPAC/cwas/cwas.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 22ed56a Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:26:54 2022 -0400 Update CPAC/cwas/cwas.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 490e319 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:26:32 2022 -0400 Update CPAC/cwas/cwas.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 8462865 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:25:57 2022 -0400 Update CPAC/resources/configs/group_config_template.yml Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 3269c0e Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:25:14 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit bb6458b Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:22:33 2022 -0400 Update CPAC/pipeline/cpac_group_runner.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit fe1dff4 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:22:25 2022 -0400 Update CPAC/cwas/cwas.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 6fcb279 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:22:10 2022 -0400 Update CPAC/cwas/cwas.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit f25b604 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:22:04 2022 -0400 Update CPAC/cwas/cwas.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 35318a5 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:21:52 2022 -0400 Update CPAC/cwas/cwas.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 6ccce46 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 17:20:28 2022 -0400 Update CPAC/cwas/cwas.py Co-authored-by: Jon Clucas <jon.clucas@childmind.org> commit 6dc4a2b Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 10:55:53 2022 -0400 Update cpac_outputs.tsv Added 2 lines for MDMR group_analysis output commit b6ed208 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 10:48:47 2022 -0400 Update group_config_template.yml commit 2ab1d64 Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Fri Oct 7 10:48:09 2022 -0400 Fixed 1.8.4 image intake Fixed the intake for images to make the 1.8.4 BIDS convention. commit 68e3416 Merge: 32632fa 9586d71 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Oct 7 10:20:22 2022 -0400 :fast_forward: Bring `develop` up to date with `main` commit c2ba9d6 Author: Jon Clucas <jon.clucas@childmind.org> Date: Wed Oct 5 15:16:39 2022 -0400 :coffin: Add placeholder default_pipeline.yml for backwards compatibility [skip ci] commit 76a4a75 Author: Jon Clucas <jon.clucas@childmind.org> Date: Wed Oct 5 17:51:41 2022 +0000 :recycle: Send 'desc-mean_bold' as input to `distcor_blip_fsl_topup` Co-authored-by: Steve Giavasis <sgiava77@gmail.com> commit 0182f98 Author: Jon Clucas <jon.clucas@childmind.org> Date: Wed Oct 5 11:12:03 2022 -0400 :memo: Add rbc-options update to CHANGELOG [skip ci] Co-authored-by: Greg Kiar <gkiar@users.noreply.github.com> commit 5208944 Author: Jon Clucas <jon.clucas@childmind.org> Date: Tue Oct 4 17:00:49 2022 -0400 :wrench: Base rbc-options on fmriprep-options Co-authored-by: Greg Kiar <gkiar@users.noreply.github.com> commit 1ab4086 Author: Jon Clucas <jon.clucas@childmind.org> Date: Tue Oct 4 20:48:57 2022 +0000 :recycle: Replumb to prevent wild TOPUP forking Co-authored-by: Steve Giavasis <sgiava77@gmail.com> commit c3ac6ac Author: diegoaper <88197703+diegoaper@users.noreply.github.com> Date: Tue Oct 4 15:48:30 2022 -0400 MDMR Group Config Template Update to the scripts and config template commit eee5461 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 30 21:21:15 2022 +0000 :recycle: Fix cyclical imports commit db27851 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 30 16:37:46 2022 -0400 :alien: Import typehints in function node commit c148153 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 30 15:41:34 2022 +0000 :loud_sound: Add FSL-`DwellTime` fix to CHANGELOG [skip ci] Co-authored-by: Nathalia Esper <nathbianchini@gmail.com> Co-authored-by: Alex Franco <eng.franco@gmail.com> commit e53581b Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 30 15:27:52 2022 +0000 :bug: Fix import path commit 2338585 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 30 15:24:38 2022 +0000 :page_facing_up: Add/update LGPL-3-or-later notice to modified files [skip ci] commit 109d536 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 30 15:11:39 2022 +0000 :recycle: Only look for `EffectiveEchoSpacing` in functional sidecar commit 695d29a Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 30 14:41:04 2022 +0000 :rotating_light: Remove duplicate good-name [skip ci] commit c9bea18 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 30 14:37:12 2022 +0000 :recycle: DRY and let `calc_delta_te_and_asym_ratio` determine EES source commit 55ca4d9 Author: Jon Clucas <jon.clucas@childmind.org> Date: Thu Sep 29 14:09:12 2022 +0000 :bug: Fix logic checking for `diffphase-effectiveEchoSpacing` commit d41dc29 Author: Jon Clucas <jon.clucas@childmind.org> Date: Wed Sep 28 12:42:26 2022 -0400 :bug: Only connect calc_delta_ratio if diff commit ca86b0b Author: Jon Clucas <jon.clucas@childmind.org> Date: Wed Sep 28 09:56:32 2022 -0400 :bug: Fix plumbing for EffectiveEchoSpacing commit f7ca070 Author: Jon Clucas <jon.clucas@childmind.org> Date: Tue Sep 27 17:26:49 2022 -0400 :recycle: Get EffectiveEchoSpacing from func metadata if possible commit 376d550 Author: Jon Clucas <jon.clucas@childmind.org> Date: Tue Sep 27 15:19:59 2022 -0400 :bug: Update DwellTime → EffectiveEchoSpacing for FSL FUGUE Co-authored-by: Nathalia Esper <nathbianchini@gmail.com> Co-authored-by: Alex Franco <eng.franco@gmail.com> commit 32632fa Merge: eed40c5 238f499 Author: Steve Giavasis <sgiava77@gmail.com> Date: Mon Sep 26 13:23:08 2022 -0400 Merge pull request #1777 from FCP-INDI/differentiate-sametime-data-configs 🐛 Differentiate sametime data and pipeline configs commit eed40c5 Merge: 76eb34d a64541e Author: Steve Giavasis <sgiava77@gmail.com> Date: Mon Sep 26 13:22:50 2022 -0400 Merge pull request #1775 from FCP-INDI/deeper-working-path 🚚 Use `f'pipeline_{pipeline_name}'` subdirectories for `log`, `working`, and `output` commit 76eb34d Author: sgiavasis <sgiava77@gmail.com> Date: Mon Sep 26 17:21:02 2022 +0000 Merge resolution for latest nuisance and native/template-space options changes. commit b30a2e0 Merge: 1e24c69 ea18242 Author: sgiavasis <sgiava77@gmail.com> Date: Sun Sep 25 08:30:26 2022 +0000 Merge branch 'dev-fix' into develop commit ea18242 Author: sgiavasis <sgiava77@gmail.com> Date: Sun Sep 25 08:27:49 2022 +0000 Staging changes from template-space derivatives for next release. commit 9c0a89c Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 23 12:48:29 2022 -0400 :bug: Create nested working directory before writing PID to disk commit d50f8da Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 23 12:26:11 2022 -0400 :recycle: Move PID on disk one level deeper in working directory commit 137c482 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 23 12:17:07 2022 -0400 :recycle: Modularize checking p_name commit 1899c9e Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 23 10:50:41 2022 -0400 :truck: Nest `failedToStart.log` as deeply as possible commit ed554a6 Merge: 0490394 a64541e Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 23 10:33:30 2022 -0400 :twisted_rightwards_arrow: Merge develop into deeper-config-path commit 238f499 Merge: 68ac96a 1e24c69 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 23 10:19:13 2022 -0400 :twisted_rightwards_arrows: Merge develop into differentiate-sametime-data-configs commit a64541e Merge: e5ec37c 1e24c69 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 23 10:14:02 2022 -0400 :twisted_rightwards_arrows: Merge develop into deeper-working-path commit 0490394 Author: Jon Clucas <jon.clucas@childmind.org> Date: Thu Sep 22 14:38:02 2022 -0400 :pencil2: Set c['subject_id'] commit f3aefca Author: Jon Clucas <jon.clucas@childmind.org> Date: Thu Sep 22 12:20:57 2022 -0400 :truck: Move C-PAC-generated data and pipeline configs one level deeper commit 2ed4d6a Author: Jon Clucas <jon.clucas@childmind.org> Date: Thu Sep 22 11:21:48 2022 -0400 :truck: Move C-PAC-generated config files into log dir commit 19c3890 Merge: e5ec37c 68ac96a Author: Jon Clucas <jon.clucas@childmind.org> Date: Thu Sep 22 10:59:04 2022 -0400 :twisted_rightwards_arrows: Merge differentiate-sametime-data-configs into deeper-config-path commit 68ac96a Author: Jon Clucas <jon.clucas@childmind.org> Date: Wed Sep 21 17:37:02 2022 -0400 :white_check_mark: Add unit test for hash_data_config commit 6003194 Author: Jon Clucas <jon.clucas@childmind.org> Date: Wed Sep 21 17:07:57 2022 -0400 :loud_sound: Add config hash string update to CHANGELOG commit e5ec37c Merge: e09cfa0 14e1591 Author: Jon Clucas <jon.clucas@childmind.org> Date: Wed Sep 21 16:36:39 2022 -0400 :twisted_rightwards_arrows: Merge develop into deeper-working-path commit e09cfa0 Author: Jon Clucas <jon.clucas@childmind.org> Date: Wed Sep 21 16:13:35 2022 -0400 :bug: Change working path update location commit 9586d71 Merge: 12c4f74 94d8082 Author: Steve Giavasis <sgiava77@gmail.com> Date: Mon Sep 19 21:31:01 2022 -0400 Merge pull request #1764 from FCP-INDI/fix/pipeline-config-versions 🔖 Hotfix: Update version to 1.8.4 commit 94d8082 Author: sgiavasis <sgiava77@gmail.com> Date: Tue Sep 20 01:27:46 2022 +0000 Fix Neurostars link in the README. commit 8804f61 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 16 15:23:00 2022 -0400 :art: Rename `f'cpac_{pipeline_name}'` directories to `f'pipeline_{pipeline_name}'` to match `output`, `log`, and `working` subdirectories Co-authored-by: Steve Giavasis <sgiava77@gmail.com> commit 77a1c5c Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 16 15:13:12 2022 -0400 :truck: Add pipeline-config-level directory for participant working directories commit 7718419 Author: Jon Clucas <jon.clucas@childmind.org> Date: Fri Sep 16 14:49:31 2022 -0400 :goal_net: Sanitize `pipeline_name` during validation commit ce6dd09 Author: sgiavasis <sgiava77@gmail.com> Date: Fri Sep 9 18:51:27 2022 +0000 Updated changelog. commit 7f42613 Author: sgiavasis <sgiava77@gmail.com> Date: Fri Sep 9 18:45:47 2022 +0000 Improved the error message for missing epi field map meta-data. commit d43aa6c Author: sgiavasis <sgiava77@gmail.com> Date: Fri Sep 9 04:14:31 2022 +0000 Read in TotalReadoutTime from field map metadata, if it exists. Pass TotalReadoutTime to FSL TOPUP if present. commit 9453398 Author: Theodore (Machine User) <CMI_CPAC_Support@childmind.org> Date: Wed Aug 31 17:42:23 2022 +0000 :bookmark: Update version to 1.8.4 (:construction_worker: Differentiate between Git branches and tags for Docker tags)

[skip ci]

…bcd`

…rst_crash` Co-authored-by: Greg Kiar <gkiar@users.noreply.github.com>

…p_on_first_crash`

shnizzedy · 2022-10-31T14:46:47Z

Making this a draft again after a convo w/ Greg; going to do BBR on its own first, then this configurable to

Do second run only on failure
Choose better reg between two runs
Don't guardrail

shnizzedy and others added 30 commits September 26, 2022 16:13

🚧 WIP 🥅 Add registration guardrail

99a0ea8

♻️ Modularize mask parameter checking

8cc3f5a

🚧 WIP 🥅 Create registration guardrail

fe7413b

🔧 Add 'quality_thresholds' to 'registration_workflows' in pipeline co…

3aea371

…nfig

🔧 Set global registration QC thresholds on config load

8fa5c23

🥅 Pass registrations through guardrail before continuing

b891928

🥅 Plug in registration guardrails

3fb78f0

♻️ Convert random.log to random.tsv

c12e7c4

✨ Afford retrying registration with a different random seed

b7fabf4

🥅 Add registration guardrails (with retries) to anatomical preproc

d3bdfa8

📄 Add license notice to modified files

db3d555

[skip ci]

♻️ Plug in ants guardrail

b9a7ad0

🔥 Remove empty file

d9d0748

[skip ci]

🎨 Initialze guardrail before conditional

d61569f

🐛 Fix concat-then-guardrail logic

58811df

♻️ Give each guardrail a unique name

fe139cc

Co-authored-by: Steve Giavasis <sgiava77@gmail.com>

🎨 Keep random seed in bounds

07a91cd

🐛 Add imports to guardrail node initialization

cf8272b

👔 Change guardrail retry default to True and retry even if not chan…

cfd7a91

…ging seed Co-authored-by: Mike Milham <Michael.Milham@childmind.org> Co-authored-by: Steve Giavasis <sgiava77@gmail.com>

🐛 Handle list values returned from qc_masks

ed81db0

🐛 Log failed metric instead of boolean

e9359c2

✏️ Fix typo (octal, not hexadecimal)

f6b8540

[skip ci]

🚧 WIP 🥅 Iterate guardrail installation

6c81eec

♻️ Rewire coreg for bbreg fallback options

492c823

🩹 ~~el~~if

e8f0c32

🚨 Minor linting

1190804

♻️ Move logger import + declaration into guardrail function

66e4ce6

♻️ Better handling of global thresholds

837533e

shnizzedy and others added 22 commits October 28, 2022 14:08

📝 Fix registration docstring workflow graphs

056afa2

[skip ci]

📄 Move license declaration from docstring to comments

dda6eb0

[skip ci]

⏪ Remove prototype guardrails from freesurfer*connector functions

65b7bf2

🥅 Guardrail freesurfer_fsl_brain_connector

6bd09c3

🥅 Guardrail mask_T2

243fdd9

🥅 Guardrail fnirt_based_brain_extraction

1cbf464

🥅 Guardrail freesurfer_abcd_preproc

611066f

⏪ Remove prototype guardrails from `correct_restore_brain_intensity_a…

00c3116

…bcd`

🥅 Guardrail init_brain_extraction_wf

20e87e4

🔧 Add fail_fast configuration option to expose Nipype's `stop_on_fi…

eed56b3

…rst_crash` Co-authored-by: Greg Kiar <gkiar@users.noreply.github.com>

🔥 Remove prototype guardrail definitions

5cc28cf

📝 Expand guardrail docstrings

50261d4

🥅 Guardrail distcor_blip_afni_qwarp

d4b7d02

🥅 Guardrail 'distcor_blip_fsl_topup'

8f917a7

🥅 Guardrail linear_reg_func_to_anat

744411f

🥅 Guardrail anat_refined_mask

51051d9

🥅 Guardrail bold_mask_anatomical_based

3cce875

🥅 Guardrail bold_mask_css

cde0c7c

🥅 Guardrail dual_regression

e0e2138

🥅 Guardrail spatial_regression

97fd7fb

✅ Update random seed test

307979e

fixup! 🔧 Add fail_fast configuration option to expose Nipype's `sto…

02887af

…p_on_first_crash`

shnizzedy marked this pull request as draft October 31, 2022 14:45

This was referenced Oct 31, 2022

🥅 Guardrail BBR only #1815

Draft

🔧 Add fail_fast to expose Nipype's stop_on_first_crash #1816

Merged

shnizzedy changed the base branch from develop to develop-1.8.6 December 21, 2022 18:17

shnizzedy added this to the 1.8.6 release milestone Dec 21, 2022

nx10 changed the base branch from develop-1.8.6 to develop June 1, 2023 18:06

shnizzedy removed this from the 1.8.6 release milestone Oct 27, 2023

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🥅 Add registration guardrails #1814

🥅 Add registration guardrails #1814

shnizzedy commented Oct 31, 2022 •

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shnizzedy commented Oct 31, 2022

	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

🥅 Add registration guardrails #1814

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🥅 Add registration guardrails #1814

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shnizzedy commented Oct 31, 2022 • edited Loading

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Guardrails strategy

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shnizzedy commented Oct 31, 2022

shnizzedy commented Oct 31, 2022 •

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