Merge tag '25.2.0'

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)

Author: effigies

.maint/CONTRIBUTORS.md

@@ -13,42 +13,52 @@ Before every release, unlisted contributors will be invited again to add their n
 | Bellec            | Pierre       |  | 0000-0002-9111-0699 | SIMEXP Lab, CRIUGM, University of Montréal, Montréal, Canada                                                                                 |
 | Benson            | Noah C.      |  | 0000-0002-2365-8265 | Department of Psychology, New York University                                                                                                |
 | Bhagwat           | Nikhil       |  | 0000-0001-6073-7141 | Montreal Neurological Institute, McGill University                                                                                           |
+| Blair             | Ross W.      |  | 0000-0003-3007-1056 | Department of Psychology, Stanford University                                                                                                |
 | Camacho           | Milton       |  | 0000-0002-5379-5076 | Department of Pediadrics, University of Calgary                                                                                           |
 | Callenberg        | Keith        |  | 0000-0001-7786-9300 | Department of Psychiatry, University of Pittsburgh                                                                                           |
 | Cieslak           | Matthew      |  | 0000-0002-1931-4734 | Perelman School of Medicine, University of Pennsylvania, PA, USA                                                                             |
-| de la Vega        | Alejandro    |  | 0000-0001-9062-3778 | University of Texas at Austin                                                                                                                |
+| Ciric             | Rastko       |  | 0000-0001-6347-7939 | Department of Psychology, Stanford University                                                                                                |
 | Devenyi           | Grabriel A.  |  | 0000-0002-7766-1187 | Department of Psychiatry, McGill University                                                                                                  |
+| DuPre             | Elizabeth    |  | 0000-0003-1358-196X | SIMEXP Lab, CRIUGM, University of Montréal, Montréal, Canada                                                                                 |
+| de la Vega        | Alejandro    |  | 0000-0001-9062-3778 | University of Texas at Austin                                                                                                                |
 | Erramuzpe         | Asier        |  | 0000-0002-9402-2184 | Computational Neuroimaging Lab, BioCruces Health Research Institute                                                                          |
 | Feingold          | Franklin     |  | 0000-0002-6533-2909 | Department of Psychology, Stanford University                                                                                                |
 | Finc              | Karolina     |  | 0000-0002-0157-030X | Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń                                                    |
 | Frederick         | Blaise B.    |  | 0000-0001-5832-5279 | McLean Hospital Brain Imaging Center, MA, USA                                                                                                |
 | Gau               | Rémi        |  | 0000-0002-1535-9767 | Neuro Data Science ORIGAMI Laboratory, McConnell Brain Imaging Centre, Faculty of Medicine, McGill University, Montréal, Canada             |
-| Groen             | Iris I. A.   |  | 0000-0002-5536-6128 | Department of Psychology, New York University, NY, USA                                                                                       |
-| Gomez             | Daniel E. P. |  | 0000-0001-8635-021X | Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen                                                            |
 | Ghosh             | Satrajit S.  |  | 0000-0002-5312-6729 | McGovern Institute for Brain Research, MIT, MA, USA                                                                                          |
+| Gomez             | Daniel E. P. |  | 0000-0001-8635-021X | Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen                                                            |
+| Gorgolewski       | Krzysztof J. |  | 0000-0003-3321-7583 | Department of Psychology, Stanford University                                                                                                |
+| Groen             | Iris I. A.   |  | 0000-0002-5536-6128 | Department of Psychology, New York University, NY, USA                                                                                       |
 | Halchenko         | Yaroslav O.  |  | 0000-0003-3456-2493 | Dartmouth College: Hanover, NH, United States                                                                                                |
 | Heinsfeld         | Anibal S.    |  | 0000-0002-2050-0614 | Child Mind Institute                                                                                                                         |
 | Isik              | Ayse Ilkay   |  | 0000-0002-1652-9297 | Max Planck Institute for Empirical Aesthetics                                                                                                |
 | Jacoby            | Nir          |  | 0000-0001-7936-9991 | Department of Psychology, Columbia University                                                                                                |
 | Jamison           | Keith W.     |  | 0000-0001-7139-6661 | Department of Radiology, Weill Cornell Medicine                                                                                              |
+| Kent              | James D.     |  | 0000-0002-4892-2659 | University of Texas at Austin                                                                                                                |
 | Kruper            | John         |  | 0000-0003-0081-391X | Department of Psychology, University of Washington                                                                                           |
 | Legarreta Gorroño | Jon Haitz    | @jhlegarreta | 0000-0002-9661-1396 | Brigham and Women's Hospital, Mass General Brigham, Harvard Medical School, MA, USA |
 | Liem              | Franz        |  | 0000-0003-0646-4810 | URPP Dynamics of Healthy Aging, University of Zurich                                                                                         |
 | Lurie             | Daniel J.    |  | 0000-0001-8012-6399 | Department of Psychology, University of California, Berkeley                                                                                 |
 | Ma                | Feilong      |  | 0000-0002-6838-3971 | Dartmouth College: Hanover, NH, United States                                                                                                |
 | Madison           | Thomas       |  | 0000-0003-3030-6580 | Department of Pediatrics, University of Minnesota, MN, USA                                                                                   |
+| Meisler           | Steven       | @smeisler | 0000-0002-8888-1572 |  Department of Psychiatry, University of Pennsylvania |
 | Mentch            | Jeff         |  | 0000-0002-7762-8678 | Speech & Hearing Bioscience & Technology Program, Harvard University                                                                         |
 | Moodie            | Craig A.     |  | 0000-0003-0867-1469 | Department of Psychology, Stanford University                                                                                                |
 | Naveau            | Mikaël       |  | 0000-0001-6948-9068 | Cyceron, UMS 3408 (CNRS - UCBN), France                                                                                                      |
+| Naze              | Sebastien    | @sebnaze | 0000-0003-0367-402X | QIMR Berghofer, Brisbane, Australia |
 | Nielson           | Dylan M.     |  | 0000-0003-4613-6643 | Machine Learning Team, National Institute of Mental Health, USA                                                                              |
 | Nitsch            | Alexander    |  | 0000-0002-5740-9451 | Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany                                                                |
 | Papadopoulos      | Dimitri      |  | 0000-0002-1242-8990 | Neurospin, CEA                                                                                                                               |
+| Pinsard           | Basile       | @bpinsard | 0000-0002-4391-3075 | Université de Montréal, Montreal, QC, CA |
 | Plunkett          | Dillon       |  | 0000-0001-7822-6024 | Department of Psychology, Harvard University                                                                                                 |
 | Provins           | Céline       |  | 0000-0002-1668-9629 | Department of Radiology, Lausanne University Hospital and University of Lausanne                                                             |
 | Rivera-Dompenciel | Adriana      |  | 0000-0002-3339-4857 | Neuroscience Program, University of Iowa                                                                                                     |
 | Sadil             | Patrick      |  | 0000-0003-4141-1343 | Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, MD, USA                                                        |
+| Salo              | Taylor       |  | 0000-0001-9813-3167 | Perelman School of Medicine, University of Pennsylvania, PA, USA                                                                             |
 | Satterthwaite     | Theodore D.  |  | 0000-0001-7072-9399 | Perelman School of Medicine, University of Pennsylvania, PA, USA                                                                             |
 | Schaefer          | Theo A.J.    |  | 0000-0003-4102-559X | Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany                                                                |
+| Seeley            | Saren        | @sarenseeley | 0000-0002-9493-8512 | Department of Psychiatry, Icahn School of Medicine at Mount Sinai |
 | Sitek             | Kevin R.     |  | 0000-0002-2172-5786 | Speech & Hearing Bioscience & Technology Program, Harvard University                                                                         |
 | Smith             | Robert E.    |  | 0000-0003-3636-4642 | Florey Institute of Neuroscience and Mental Health                                                                                           |
 | Sneve             | Markus H.    |  | 0000-0001-7644-7915 | Center for Lifespan Changes in Brain and Cognition, University of Oslo                                                                       |

.maint/MAINTAINERS.md

@@ -12,4 +12,3 @@ If you are participating because of your affiliation with another organization (
 | Markiewicz | Christopher J. | @effigies | 0000-0002-6533-164X | Department of Psychology, Stanford University, CA, USA | |
 | Goncalves | Mathias | @mgxd | 0000-0002-7252-7771 | Department of Psychology, Stanford University, CA, USA | |
 | Esteban | Oscar | @oesteban | 0000-0001-8435-6191 | Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland | |
-| Pinsard | Basile | @bpinsard | 0000-0002-4391-3075 | Université de Montréal, Montreal, QC, CA | 20.2.x LTS maintainer |

.maint/PIs.md

@@ -10,8 +10,8 @@ If you are participating because of your affiliation with another organization (
 
 | **Lastname** | **Name** | **Handle** | **ORCID** | **Affiliation** | **Position** |
 | --- | --- | --- | --- | --- | --- |
-| Esteban | Oscar | @oesteban | 0000-0001-8435-6191 | Department of Radiology, Lausanne University Hospital and University of Lausanne |  |
 | Milham | Michael P. |  | 0000-0003-3532-1210 | Child Mind Institute |  |
-| Poldrack | Russell A. | @poldrack | 0000-0001-6755-0259 | Department of Psychology, Stanford University, CA, USA | -1 |
-| Rokem | Ariel | @arokem | 0000-0003-0679-1985 | The University of Washington eScience Institute, WA, USA |  |
 | Satterthwaite | Theodore D. |  | 0000-0001-7072-9399 | Perelman School of Medicine, University of Pennsylvania, PA, USA |  |
+| Rokem | Ariel | @arokem | 0000-0003-0679-1985 | The University of Washington eScience Institute, WA, USA |  |
+| Poldrack | Russell A. | @poldrack | 0000-0001-6755-0259 | Department of Psychology, Stanford University, CA, USA | -1 |
+| Esteban | Oscar | @oesteban | 0000-0001-8435-6191 | Department of Radiology, Lausanne University Hospital and University of Lausanne |  |