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Closes #3496.

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codecov bot commented Aug 15, 2025

Codecov Report

❌ Patch coverage is 88.88889% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 73.56%. Comparing base (c961b3c) to head (3ea4c4c).
⚠️ Report is 195 commits behind head on master.

Files with missing lines Patch % Lines
fmriprep/workflows/bold/registration.py 88.88% 2 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master    #3500      +/-   ##
==========================================
+ Coverage   73.50%   73.56%   +0.06%     
==========================================
  Files          60       60              
  Lines        4582     4600      +18     
  Branches      585      585              
==========================================
+ Hits         3368     3384      +16     
- Misses       1085     1087       +2     
  Partials      129      129              

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https://output.circle-artifacts.com/output/job/6c4e4e34-c826-457a-9d1f-11cdf635de1e/artifacts/0/tmp/ds054/fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json:

{
  "GeneratedBy": [
    {
      "Name": "mri_coreg",
      "Version": "7.3.2"
    }
  ],
  "Sources": [
    "bids::sub-100185/func/sub-100185_task-machinegame_run-01_desc-coreg_boldref.nii.gz"
  ]
}

https://output.circle-artifacts.com/output/job/955df01f-5407-454f-899b-3d65cd9c1aff/artifacts/0/tmp/ds210/fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json:

{
  "GeneratedBy": [
    {
      "Name": "mri_coreg",
      "Version": "7.3.2"
    }
  ],
  "Sources": [
    "bids::sub-02/func/sub-02_task-cuedSGT_run-01_desc-coreg_boldref.nii.gz"
  ]
}

https://output.circle-artifacts.com/output/job/95d2b2bf-3ffc-4bc1-a46b-8f9a4861d325/artifacts/0/full-run/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json:

{
  "FinalCost": 0.649006,
  "GeneratedBy": [
    {
      "Name": "bbregister",
      "Version": "7.3.2"
    }
  ],
  "Sources": [
    "bids::sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-coreg_boldref.nii.gz"
  ]
}

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forgot to finalize this

@effigies effigies merged commit 03e209f into nipreps:master Aug 19, 2025
21 checks passed
@effigies effigies deleted the feat/mincost branch August 19, 2025 15:55
effigies added a commit that referenced this pull request Oct 1, 2025
25.2.0 (October 01, 2025)

New feature release in the 25.2.x series.

This release is an *fMRIPrep Long-Term Support (LTS)* release.
The planned support window is 4 years, until October 2029.

This release is an incremental improvement over 25.1.x, but includes some fixes
and improvements that do not fit within our
`bug-fix policy <https://www.nipreps.org/devs/releases/#bug-fix-releases>`__.

Importantly, the change in interpolation in 25.1.0 introduced artifacts for some datasets.
This release changes the default interpolation mode to ``grid-constant``, which
resolves those problems while not reintroducing the issue the previous release sought to fix.

This release also (finally) introduces per-session processing.
The ``--session-label`` flag selects the sessions to process,
and the ``--subject-anatomical-reference`` flag indicates whether and how
to combine across sessions.
Existing filters passed via ``--bids-filter-file`` may need to be updated or
removed in favor of using these flags to achieve the desired behavior.

We would like to thank the AMP-SCZ and ENIGMA consortia for testing out and providing
feedback on this release.

  * FIX: Clean up output report language (#3529)
  * FIX: Default to grid-constant interpolation mode (#3516)
  * FIX: Adapt to transposed ndcoords in nitransforms (#3517)
  * FIX: Write out Freesurfer-derived outputs (#3512)
  * FIX: Add kwargs to _warnings.py (#3483)
  * ENH: Resample BOLD data to any surface template space using the Connectome Workbench (#3461)
  * ENH: Add boldref / sbref to source metadata (#3532)
  * ENH: Add dedicated session filtering, alternative anatomical template options (#3495)
  * ENH: Write out goodvoxels mask (#3513)
  * ENH: Add registration metadata to boldref-to-anat transforms (#3500)
  * ENH: Write out cortex mask GIFTIs (#3491)
  * ENH: Update transforms.py according to new transform chain of nitransforms (#3494)
  * RF/DOC: Improve and document command-line parser defaults (#3487)
  * DOC: Explain better SDC and B0FieldSource requirement (#2768)
  * DOC: Document `freesurfer` parameter in BOLD confound workflow init (#3504)
  * DOC: Add myself to contributor list (#3506)
  * DOC: Fix non-standard Input/Output docstring section management (#3505)
  * MNT: Split Dockerfile into base and pixi layers (#3521)
  * MNT: Replace conda with pixi and lock (#3503)
  * MNT: Update license metadata using SPDX expression (#3486)
  * MNT: no need to re-run `ruff check` after `ruff format` (#3480)
  * MNT: Update pre-commit ruff legacy alias (#3479)
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Save registration program and final cost to xfm.json metadata

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