…nfig

[skip ci]

[skip ci]

Co-authored-by: Steve Giavasis <[email protected]>

…ging seed

Co-authored-by: Mike Milham <[email protected]>
Co-authored-by: Steve Giavasis <[email protected]>

Squashed commit of the following:

commit 356dc30
Merge: b1ce64b 55667a2
Author: Steve Giavasis <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Fri Oct 14 16:03:28 2022 -0400

    Merge branch 'develop' into feature/total_readout_time

commit 8301e3c
Author: Steve Giavasis <[email protected]>
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 <[email protected]>
Date:   Fri Oct 14 15:55:55 2022 -0400

    :art: Include minimized pipeline config in hardlinking step

commit a641d00
Author: Jon Clucas <[email protected]>
Date:   Fri Oct 14 15:44:42 2022 -0400

    :lock: Make generated config files read-only

    Co-authored-by: Steve Giavasis <[email protected]>

commit 37a6874
Merge: b5d0d1f 5b2465f
Author: Steve Giavasis <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Fri Oct 14 15:18:31 2022 -0400

    Merge branch 'develop' into bugfix/random_seed

commit 7f50838
Merge: 8ebf0a7 c2ba9d6
Author: Steve Giavasis <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Thu Oct 13 16:55:12 2022 -0400

    move changelog entry to the unreleased section

commit b5c742a
Author: Connor Lane <[email protected]>
Date:   Wed Oct 12 17:43:26 2022 -0400

    update changelog

commit 6b402b0
Author: Jon Clucas <[email protected]>
Date:   Wed Oct 12 16:12:59 2022 -0400

    fixup! :fast_forward: Bring `develop` up to date with `main`

commit 5867210
Author: Connor Lane <[email protected]>
Date:   Wed Oct 12 09:48:39 2022 -0400

    :bug: fix type handling in `set_up_random_state`

commit 5b2465f
Author: diegoaper <[email protected]>
Date:   Tue Oct 11 11:48:57 2022 -0400

    Removed participant Configuration

commit 92f9658
Author: diegoaper <[email protected]>
Date:   Mon Oct 10 14:09:46 2022 -0400

    Update cpac_group_runner.py

commit a112d34
Author: diegoaper <[email protected]>
Date:   Mon Oct 10 10:40:56 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 031946a
Author: diegoaper <[email protected]>
Date:   Mon Oct 10 10:40:35 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit df2bb33
Author: diegoaper <[email protected]>
Date:   Mon Oct 10 10:40:00 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit c5d306d
Author: diegoaper <[email protected]>
Date:   Mon Oct 10 10:39:46 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit e903b98
Author: diegoaper <[email protected]>
Date:   Mon Oct 10 10:39:16 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 82e2ece
Author: diegoaper <[email protected]>
Date:   Mon Oct 10 10:38:50 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit d75dbe3
Author: diegoaper <[email protected]>
Date:   Mon Oct 10 10:38:32 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 9407c63
Author: diegoaper <[email protected]>
Date:   Mon Oct 10 10:38:11 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 61097e3
Merge: 0ba271a 750c9ec
Author: diegoaper <[email protected]>
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 <[email protected]>
Date:   Mon Oct 10 10:37:29 2022 -0400

    Update cpac_group_runner.py

commit 750c9ec
Author: diegoaper <[email protected]>
Date:   Mon Oct 10 10:37:04 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit cf81d08
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:36:52 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit e570fbf
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:36:38 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 2eea1f4
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:35:59 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 99620c6
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:35:44 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit cf8f0d9
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:33:11 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit de6235f
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:32:40 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit ebe6a27
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:32:26 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit c50db8d
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:30:13 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 748f376
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:29:26 2022 -0400

    Update CPAC/cwas/pipeline.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 6d938f4
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:28:55 2022 -0400

    Update CPAC/cwas/pipeline.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 0b2b868
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:28:20 2022 -0400

    Update CPAC/cwas/pipeline.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 281427d
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:27:24 2022 -0400

    Update CPAC/cwas/cwas.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 63c3ad4
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:27:15 2022 -0400

    Update CPAC/cwas/cwas.py

    Co-authored-by: Jon Clucas <[email protected]>

commit ca75679
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:27:05 2022 -0400

    Update CPAC/cwas/cwas.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 22ed56a
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:26:54 2022 -0400

    Update CPAC/cwas/cwas.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 490e319
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:26:32 2022 -0400

    Update CPAC/cwas/cwas.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 8462865
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:25:57 2022 -0400

    Update CPAC/resources/configs/group_config_template.yml

    Co-authored-by: Jon Clucas <[email protected]>

commit 3269c0e
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:25:14 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit bb6458b
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:22:33 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit fe1dff4
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:22:25 2022 -0400

    Update CPAC/cwas/cwas.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 6fcb279
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:22:10 2022 -0400

    Update CPAC/cwas/cwas.py

    Co-authored-by: Jon Clucas <[email protected]>

commit f25b604
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:22:04 2022 -0400

    Update CPAC/cwas/cwas.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 35318a5
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:21:52 2022 -0400

    Update CPAC/cwas/cwas.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 6ccce46
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:20:28 2022 -0400

    Update CPAC/cwas/cwas.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 6dc4a2b
Author: diegoaper <[email protected]>
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 <[email protected]>
Date:   Fri Oct 7 10:48:47 2022 -0400

    Update group_config_template.yml

commit 2ab1d64
Author: diegoaper <[email protected]>
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 <[email protected]>
Date:   Fri Oct 7 10:20:22 2022 -0400

    :fast_forward: Bring `develop` up to date with `main`

commit c2ba9d6
Author: Jon Clucas <[email protected]>
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 <[email protected]>
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 <[email protected]>

commit 0182f98
Author: Jon Clucas <[email protected]>
Date:   Wed Oct 5 11:12:03 2022 -0400

    :memo: Add rbc-options update to CHANGELOG

    [skip ci]

    Co-authored-by: Greg Kiar <[email protected]>

commit 5208944
Author: Jon Clucas <[email protected]>
Date:   Tue Oct 4 17:00:49 2022 -0400

    :wrench: Base rbc-options on fmriprep-options

    Co-authored-by: Greg Kiar <[email protected]>

commit 1ab4086
Author: Jon Clucas <[email protected]>
Date:   Tue Oct 4 20:48:57 2022 +0000

    :recycle: Replumb to prevent wild TOPUP forking

    Co-authored-by: Steve Giavasis <[email protected]>

commit c3ac6ac
Author: diegoaper <[email protected]>
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 <[email protected]>
Date:   Fri Sep 30 21:21:15 2022 +0000

    :recycle: Fix cyclical imports

commit db27851
Author: Jon Clucas <[email protected]>
Date:   Fri Sep 30 16:37:46 2022 -0400

    :alien: Import typehints in function node

commit c148153
Author: Jon Clucas <[email protected]>
Date:   Fri Sep 30 15:41:34 2022 +0000

    :loud_sound: Add FSL-`DwellTime` fix to CHANGELOG

    [skip ci]

    Co-authored-by: Nathalia Esper <[email protected]>
    Co-authored-by: Alex Franco <[email protected]>

commit e53581b
Author: Jon Clucas <[email protected]>
Date:   Fri Sep 30 15:27:52 2022 +0000

    :bug: Fix import path

commit 2338585
Author: Jon Clucas <[email protected]>
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 <[email protected]>
Date:   Fri Sep 30 15:11:39 2022 +0000

    :recycle: Only look for `EffectiveEchoSpacing` in functional sidecar

commit 695d29a
Author: Jon Clucas <[email protected]>
Date:   Fri Sep 30 14:41:04 2022 +0000

    :rotating_light: Remove duplicate good-name

    [skip ci]

commit c9bea18
Author: Jon Clucas <[email protected]>
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 <[email protected]>
Date:   Thu Sep 29 14:09:12 2022 +0000

    :bug: Fix logic checking for `diffphase-effectiveEchoSpacing`

commit d41dc29
Author: Jon Clucas <[email protected]>
Date:   Wed Sep 28 12:42:26 2022 -0400

    :bug: Only connect calc_delta_ratio if diff

commit ca86b0b
Author: Jon Clucas <[email protected]>
Date:   Wed Sep 28 09:56:32 2022 -0400

    :bug: Fix plumbing for EffectiveEchoSpacing

commit f7ca070
Author: Jon Clucas <[email protected]>
Date:   Tue Sep 27 17:26:49 2022 -0400

    :recycle: Get EffectiveEchoSpacing from func metadata if possible

commit 376d550
Author: Jon Clucas <[email protected]>
Date:   Tue Sep 27 15:19:59 2022 -0400

    :bug: Update DwellTime → EffectiveEchoSpacing for FSL FUGUE

    Co-authored-by: Nathalia Esper <[email protected]>
    Co-authored-by: Alex Franco <[email protected]>

commit 32632fa
Merge: eed40c5 238f499
Author: Steve Giavasis <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Sun Sep 25 08:30:26 2022 +0000

    Merge branch 'dev-fix' into develop

commit ea18242
Author: sgiavasis <[email protected]>
Date:   Sun Sep 25 08:27:49 2022 +0000

    Staging changes from template-space derivatives for next release.

commit 9c0a89c
Author: Jon Clucas <[email protected]>
Date:   Fri Sep 23 12:48:29 2022 -0400

    :bug: Create nested working directory before writing PID to disk

commit d50f8da
Author: Jon Clucas <[email protected]>
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 <[email protected]>
Date:   Fri Sep 23 12:17:07 2022 -0400

    :recycle: Modularize checking p_name

commit 1899c9e
Author: Jon Clucas <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Fri Sep 23 10:14:02 2022 -0400

    :twisted_rightwards_arrows: Merge develop into deeper-working-path

commit 0490394
Author: Jon Clucas <[email protected]>
Date:   Thu Sep 22 14:38:02 2022 -0400

    :pencil2: Set c['subject_id']

commit f3aefca
Author: Jon Clucas <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Wed Sep 21 17:37:02 2022 -0400

    :white_check_mark: Add unit test for hash_data_config

commit 6003194
Author: Jon Clucas <[email protected]>
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 <[email protected]>
Date:   Wed Sep 21 16:36:39 2022 -0400

    :twisted_rightwards_arrows: Merge develop into deeper-working-path

commit e09cfa0
Author: Jon Clucas <[email protected]>
Date:   Wed Sep 21 16:13:35 2022 -0400

    :bug: Change working path update location

commit 9586d71
Merge: 12c4f74 94d8082
Author: Steve Giavasis <[email protected]>
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 <[email protected]>
Date:   Tue Sep 20 01:27:46 2022 +0000

    Fix Neurostars link in the README.

commit 8804f61
Author: Jon Clucas <[email protected]>
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 <[email protected]>

commit 77a1c5c
Author: Jon Clucas <[email protected]>
Date:   Fri Sep 16 15:13:12 2022 -0400

    :truck: Add pipeline-config-level directory for participant working directories

commit 7718419
Author: Jon Clucas <[email protected]>
Date:   Fri Sep 16 14:49:31 2022 -0400

    :goal_net: Sanitize `pipeline_name` during validation

commit ce6dd09
Author: sgiavasis <[email protected]>
Date:   Fri Sep 9 18:51:27 2022 +0000

    Updated changelog.

commit 7f42613
Author: sgiavasis <[email protected]>
Date:   Fri Sep 9 18:45:47 2022 +0000

    Improved the error message for missing epi field map meta-data.

commit d43aa6c
Author: sgiavasis <[email protected]>
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) <[email protected]>
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 <[email protected]>
Date:   Tue Oct 18 14:36:38 2022 -0400

    :truck: Include graph2use in graph filenames

commit b132f10
Author: Jon Clucas <[email protected]>
Date:   Tue Oct 18 12:32:44 2022 -0400

    :wrench: Add graphviz options to pipeline config

commit a72f1a6
Author: Jon Clucas <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Fri Oct 14 16:03:28 2022 -0400

    Merge branch 'develop' into feature/total_readout_time

commit 8301e3c
Author: Steve Giavasis <[email protected]>
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 <[email protected]>
Date:   Fri Oct 14 15:55:55 2022 -0400

    :art: Include minimized pipeline config in hardlinking step

commit a641d00
Author: Jon Clucas <[email protected]>
Date:   Fri Oct 14 15:44:42 2022 -0400

    :lock: Make generated config files read-only

    Co-authored-by: Steve Giavasis <[email protected]>

commit 37a6874
Merge: b5d0d1f 5b2465f
Author: Steve Giavasis <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Fri Oct 14 15:18:31 2022 -0400

    Merge branch 'develop' into bugfix/random_seed

commit 7f50838
Merge: 8ebf0a7 c2ba9d6
Author: Steve Giavasis <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Thu Oct 13 16:55:12 2022 -0400

    move changelog entry to the unreleased section

commit b5c742a
Author: Connor Lane <[email protected]>
Date:   Wed Oct 12 17:43:26 2022 -0400

    update changelog

commit 6b402b0
Author: Jon Clucas <[email protected]>
Date:   Wed Oct 12 16:12:59 2022 -0400

    fixup! :fast_forward: Bring `develop` up to date with `main`

commit 5867210
Author: Connor Lane <[email protected]>
Date:   Wed Oct 12 09:48:39 2022 -0400

    :bug: fix type handling in `set_up_random_state`

commit 5b2465f
Author: diegoaper <[email protected]>
Date:   Tue Oct 11 11:48:57 2022 -0400

    Removed participant Configuration

commit 92f9658
Author: diegoaper <[email protected]>
Date:   Mon Oct 10 14:09:46 2022 -0400

    Update cpac_group_runner.py

commit a112d34
Author: diegoaper <[email protected]>
Date:   Mon Oct 10 10:40:56 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 031946a
Author: diegoaper <[email protected]>
Date:   Mon Oct 10 10:40:35 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit df2bb33
Author: diegoaper <[email protected]>
Date:   Mon Oct 10 10:40:00 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit c5d306d
Author: diegoaper <[email protected]>
Date:   Mon Oct 10 10:39:46 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit e903b98
Author: diegoaper <[email protected]>
Date:   Mon Oct 10 10:39:16 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 82e2ece
Author: diegoaper <[email protected]>
Date:   Mon Oct 10 10:38:50 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit d75dbe3
Author: diegoaper <[email protected]>
Date:   Mon Oct 10 10:38:32 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 9407c63
Author: diegoaper <[email protected]>
Date:   Mon Oct 10 10:38:11 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 61097e3
Merge: 0ba271a 750c9ec
Author: diegoaper <[email protected]>
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 <[email protected]>
Date:   Mon Oct 10 10:37:29 2022 -0400

    Update cpac_group_runner.py

commit 750c9ec
Author: diegoaper <[email protected]>
Date:   Mon Oct 10 10:37:04 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit cf81d08
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:36:52 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit e570fbf
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:36:38 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 2eea1f4
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:35:59 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 99620c6
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:35:44 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit cf8f0d9
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:33:11 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit de6235f
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:32:40 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit ebe6a27
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:32:26 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit c50db8d
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:30:13 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 748f376
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:29:26 2022 -0400

    Update CPAC/cwas/pipeline.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 6d938f4
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:28:55 2022 -0400

    Update CPAC/cwas/pipeline.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 0b2b868
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:28:20 2022 -0400

    Update CPAC/cwas/pipeline.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 281427d
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:27:24 2022 -0400

    Update CPAC/cwas/cwas.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 63c3ad4
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:27:15 2022 -0400

    Update CPAC/cwas/cwas.py

    Co-authored-by: Jon Clucas <[email protected]>

commit ca75679
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:27:05 2022 -0400

    Update CPAC/cwas/cwas.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 22ed56a
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:26:54 2022 -0400

    Update CPAC/cwas/cwas.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 490e319
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:26:32 2022 -0400

    Update CPAC/cwas/cwas.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 8462865
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:25:57 2022 -0400

    Update CPAC/resources/configs/group_config_template.yml

    Co-authored-by: Jon Clucas <[email protected]>

commit 3269c0e
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:25:14 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit bb6458b
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:22:33 2022 -0400

    Update CPAC/pipeline/cpac_group_runner.py

    Co-authored-by: Jon Clucas <[email protected]>

commit fe1dff4
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:22:25 2022 -0400

    Update CPAC/cwas/cwas.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 6fcb279
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:22:10 2022 -0400

    Update CPAC/cwas/cwas.py

    Co-authored-by: Jon Clucas <[email protected]>

commit f25b604
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:22:04 2022 -0400

    Update CPAC/cwas/cwas.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 35318a5
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:21:52 2022 -0400

    Update CPAC/cwas/cwas.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 6ccce46
Author: diegoaper <[email protected]>
Date:   Fri Oct 7 17:20:28 2022 -0400

    Update CPAC/cwas/cwas.py

    Co-authored-by: Jon Clucas <[email protected]>

commit 6dc4a2b
Author: diegoaper <[email protected]>
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 <[email protected]>
Date:   Fri Oct 7 10:48:47 2022 -0400

    Update group_config_template.yml

commit 2ab1d64
Author: diegoaper <[email protected]>
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 <[email protected]>
Date:   Fri Oct 7 10:20:22 2022 -0400

    :fast_forward: Bring `develop` up to date with `main`

commit c2ba9d6
Author: Jon Clucas <[email protected]>
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 <[email protected]>
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 <[email protected]>

commit 0182f98
Author: Jon Clucas <[email protected]>
Date:   Wed Oct 5 11:12:03 2022 -0400

    :memo: Add rbc-options update to CHANGELOG

    [skip ci]

    Co-authored-by: Greg Kiar <[email protected]>

commit 5208944
Author: Jon Clucas <[email protected]>
Date:   Tue Oct 4 17:00:49 2022 -0400

    :wrench: Base rbc-options on fmriprep-options

    Co-authored-by: Greg Kiar <[email protected]>

commit 1ab4086
Author: Jon Clucas <[email protected]>
Date:   Tue Oct 4 20:48:57 2022 +0000

    :recycle: Replumb to prevent wild TOPUP forking

    Co-authored-by: Steve Giavasis <[email protected]>

commit c3ac6ac
Author: diegoaper <[email protected]>
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 <[email protected]>
Date:   Fri Sep 30 21:21:15 2022 +0000

    :recycle: Fix cyclical imports

commit db27851
Author: Jon Clucas <[email protected]>
Date:   Fri Sep 30 16:37:46 2022 -0400

    :alien: Import typehints in function node

commit c148153
Author: Jon Clucas <[email protected]>
Date:   Fri Sep 30 15:41:34 2022 +0000

    :loud_sound: Add FSL-`DwellTime` fix to CHANGELOG

    [skip ci]

    Co-authored-by: Nathalia Esper <[email protected]>
    Co-authored-by: Alex Franco <[email protected]>

commit e53581b
Author: Jon Clucas <[email protected]>
Date:   Fri Sep 30 15:27:52 2022 +0000

    :bug: Fix import path

commit 2338585
Author: Jon Clucas <[email protected]>
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 <[email protected]>
Date:   Fri Sep 30 15:11:39 2022 +0000

    :recycle: Only look for `EffectiveEchoSpacing` in functional sidecar

commit 695d29a
Author: Jon Clucas <[email protected]>
Date:   Fri Sep 30 14:41:04 2022 +0000

    :rotating_light: Remove duplicate good-name

    [skip ci]

commit c9bea18
Author: Jon Clucas <[email protected]>
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 <[email protected]>
Date:   Thu Sep 29 14:09:12 2022 +0000

    :bug: Fix logic checking for `diffphase-effectiveEchoSpacing`

commit d41dc29
Author: Jon Clucas <[email protected]>
Date:   Wed Sep 28 12:42:26 2022 -0400

    :bug: Only connect calc_delta_ratio if diff

commit ca86b0b
Author: Jon Clucas <[email protected]>
Date:   Wed Sep 28 09:56:32 2022 -0400

    :bug: Fix plumbing for EffectiveEchoSpacing

commit f7ca070
Author: Jon Clucas <[email protected]>
Date:   Tue Sep 27 17:26:49 2022 -0400

    :recycle: Get EffectiveEchoSpacing from func metadata if possible

commit 376d550
Author: Jon Clucas <[email protected]>
Date:   Tue Sep 27 15:19:59 2022 -0400

    :bug: Update DwellTime → EffectiveEchoSpacing for FSL FUGUE

    Co-authored-by: Nathalia Esper <[email protected]>
    Co-authored-by: Alex Franco <[email protected]>

commit 32632fa
Merge: eed40c5 238f499
Author: Steve Giavasis <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Sun Sep 25 08:30:26 2022 +0000

    Merge branch 'dev-fix' into develop

commit ea18242
Author: sgiavasis <[email protected]>
Date:   Sun Sep 25 08:27:49 2022 +0000

    Staging changes from template-space derivatives for next release.

commit 9c0a89c
Author: Jon Clucas <[email protected]>
Date:   Fri Sep 23 12:48:29 2022 -0400

    :bug: Create nested working directory before writing PID to disk

commit d50f8da
Author: Jon Clucas <[email protected]>
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 <[email protected]>
Date:   Fri Sep 23 12:17:07 2022 -0400

    :recycle: Modularize checking p_name

commit 1899c9e
Author: Jon Clucas <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Fri Sep 23 10:14:02 2022 -0400

    :twisted_rightwards_arrows: Merge develop into deeper-working-path

commit 0490394
Author: Jon Clucas <[email protected]>
Date:   Thu Sep 22 14:38:02 2022 -0400

    :pencil2: Set c['subject_id']

commit f3aefca
Author: Jon Clucas <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Wed Sep 21 17:37:02 2022 -0400

    :white_check_mark: Add unit test for hash_data_config

commit 6003194
Author: Jon Clucas <[email protected]>
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 <[email protected]>
Date:   Wed Sep 21 16:36:39 2022 -0400

    :twisted_rightwards_arrows: Merge develop into deeper-working-path

commit e09cfa0
Author: Jon Clucas <[email protected]>
Date:   Wed Sep 21 16:13:35 2022 -0400

    :bug: Change working path update location

commit 9586d71
Merge: 12c4f74 94d8082
Author: Steve Giavasis <[email protected]>
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 <[email protected]>
Date:   Tue Sep 20 01:27:46 2022 +0000

    Fix Neurostars link in the README.

commit 8804f61
Author: Jon Clucas <[email protected]>
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 <[email protected]>

commit 77a1c5c
Author: Jon Clucas <[email protected]>
Date:   Fri Sep 16 15:13:12 2022 -0400

    :truck: Add pipeline-config-level directory for participant working directories

commit 7718419
Author: Jon Clucas <[email protected]>
Date:   Fri Sep 16 14:49:31 2022 -0400

    :goal_net: Sanitize `pipeline_name` during validation

commit ce6dd09
Author: sgiavasis <[email protected]>
Date:   Fri Sep 9 18:51:27 2022 +0000

    Updated changelog.

commit 7f42613
Author: sgiavasis <[email protected]>
Date:   Fri Sep 9 18:45:47 2022 +0000

    Improved the error message for missing epi field map meta-data.

commit d43aa6c
Author: sgiavasis <[email protected]>
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) <[email protected]>
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]

[skip ci]

…bcd`

…rst_crash`

Co-authored-by: Greg Kiar <[email protected]>

…p_on_first_crash`