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ENH: Support named derivative paths #3264

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merged 13 commits into from
Mar 29, 2024
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@tsalo tsalo commented Mar 28, 2024

Closes #3260.

Changes proposed in this pull request

  • Copy over ToDict action from fmriprep-docker over to the main CLI parser.
  • Modify the Config to handle named derivative paths.
    • E.g., --derivatives anat=/path/to/smriprep --> DatasetLinks = {'anat': '/path/to/smriprep'}
  • Infer derivative name from the folder name of the derivative path if it isn't labeled.
    • E.g., --derivatives /path/to/smriprep --> DatasetLinks = {'smriprep': '/path/to/smriprep'}

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codecov bot commented Mar 28, 2024

Codecov Report

Attention: Patch coverage is 90.47619% with 4 lines in your changes are missing coverage. Please review.

Project coverage is 73.82%. Comparing base (8eb8215) to head (cedf5bc).

❗ Current head cedf5bc differs from pull request most recent head 30a7083. Consider uploading reports for the commit 30a7083 to get more accurate results

Files Patch % Lines
fmriprep/workflows/base.py 0.00% 2 Missing ⚠️
fmriprep/cli/workflow.py 0.00% 1 Missing ⚠️
fmriprep/config.py 66.66% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master    #3264      +/-   ##
==========================================
+ Coverage   73.62%   73.82%   +0.19%     
==========================================
  Files          56       56              
  Lines        4243     4279      +36     
==========================================
+ Hits         3124     3159      +35     
- Misses       1119     1120       +1     

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@tsalo tsalo marked this pull request as ready for review March 28, 2024 22:00
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tsalo and others added 2 commits March 29, 2024 10:30
@tsalo tsalo requested a review from effigies March 29, 2024 15:25
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LGTM. Small suggestion.

wrapper/src/fmriprep_docker/__main__.py Outdated Show resolved Hide resolved
@effigies effigies changed the title Support named derivative paths ENH: Support named derivative paths Mar 29, 2024
@effigies effigies merged commit ecf8580 into nipreps:master Mar 29, 2024
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@tsalo tsalo deleted the named-derivatives branch March 29, 2024 16:55
effigies added a commit that referenced this pull request Jun 17, 2024
24.0.0 (June 17, 2024)

New feature release in the 24.0.x series.

This release is an incremental improvement on 23.2.x, with some
fixes for bugs discovered in the updated workflow.

New features include separation of HTML reports by session for subjects
with many BOLD runs, a new ``--fs-no-resume`` option to improve interoperability
with less typical FreeSurfer directories, such as those generated by longitudinal
FreeSurfer or FastSurfer, and adoption of DatasetLinks and BIDS-URIs, to follow
the recommendations of recent versions of BIDS.

With thanks to Dimitri Papadopoulos, Basile Pinsard, Celine Provins, Taylor Salo
and Wang Hao-Ting for their contributions!

* FIX: Add "double" type to allowed DisplacementFieldTransform (#3287)
* FIX: Require recent templateflow, select correct aparc dseg.tsv (#3256)
* FIX: Ensure proper templates are retrieved with sloppy (#3251)
* FIX: Delete summary from functional report when separated by sessions (#3223)
* FIX: Support lists in bids filter file containing ``null`` or ``*`` (#3215)
* FIX: Re-enable anat fasttrack for dataset without t1w (#3202)
* ENH: Use BIDSURI in init_ds_boldmask_wf (#3297)
* ENH: Add templateflow to DatasetLinks (#3267)
* ENH: Track proximal sources of functional GIFTIs (#3263)
* ENH: Support named derivative paths (#3264)
* ENH: Track Sources for standard-space outputs (#3262)
* ENH: Add --fs-no-resume option to reuse existing FreeSurfer outputs without resuming (#3142)
* ENH: Use BIDS URIs to track Sources in sidecars (#3255)
* ENH: Ignore unselected subjects in BIDSLayoutIndexer (#3236)
* ENH: Add metadata for motion parameters (#3245)
* ENH: Separate anatomical and functional reports per session for densely sampled dataset (#3191)
* ENH: Leverage T2w if available for BOLD -> anat coregistration (#3208)
* RF: Fix ITK warp conversion to nitransforms format (#3300)
* RF: Load report assembler from nireports (#3177)
* DOC: Clarify ``--dvars-spike-threshold`` uses standardized DVARS (#3205)
* TST: Update test to reflect new report generation behavior (#3210)
* STY: Manual conversions to f-strings (#3241)
* STY: Apply ruff/pyupgrade rule UP031 (#3280)
* STY: Lint and style check full repository (#3221)
* STY: Adopt ruff for linting and formatting (#3206)
* MNT: Pin libitk 5.3 and note dependencies (#3298)
* MNT: Upgrade ruff pre-commit, add fixing checks (#3283)
* MNT: Complete transition from flake8/black to ruff (#3279)
* MNT: Apply Repo-Review suggestions (#3194)
* MNT: Verbatim copy of Apache license 2.0 (#3259)
* MNT: Bump cryptography from 41.0.7 to 42.0.4 (#3234)
* MNT: Drop copyright year, unused dunder fields (#3247)
* MNT: Update environment pins (#3226)
* MNT: Bump codecov/codecov-action from 3 to 4 (#3219)
* DOCKER: Restore mincinfo binary (#3249)
* CI: Move to new circle machine tags (#3248)
* CI: Avoid ruff warning (#3244)
* CI: Pass ruff tests (#3243)
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Allow --derivatives to be named
2 participants