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Merge tag '25.0.0'
25.0.0 (March 25, 2025) New feature release in the 25.0.x series. This release substantially improves support for pre-computed derivatives. Previous releases would miss some derivatives and rerun the computations. Note that derivatives from previous versions will be accepted, so it should not be necessary to recompute derivatives from previous versions. The recommended command line is:: fmriprep BIDS_DIR OUT_DIR participant --derivatives fmriprep=PRECOMP_DIR Note that multiple derivatives can be specified, for example:: fmriprep BIDS_DIR OUT_DIR participant \ anat=PRECOMPUTED_ANATOMICAL_DIR \ func=PRECOMPUTED_FUNCTIONAL_DIR When the same file is found in multiple derivatives, the last one found takes precedence. Additionally, `--force-*` flags have been consolidated into a single `--force` flag that can take multiple, space-separated arguments. Structural processing changes ----------------------------- We now output white, pial and midthickness fsLR meshes on the subject surface. Look for `sub-<subject>_hemi-<L|R>_space-fsLR_*_<surf>.surf.gii` files. Brain extraction has been modified slightly to more closely match the `antsBrainExtraction.sh` workflow distributed by ANTs. The impact should be minimal, but in rare cases this fixes a crash. Fieldmap processing changes --------------------------- SyN-SDC fieldmap filtering is now single-level, following the improvements for gradient-echo fieldmaps in 24.1. Jacobian-weighting during fieldmap unwarping is now on by default *only* for PEPolar fieldmaps. To enable for other fieldmap types, use `--force fieldmap-jacobian`. All merged pull requests ------------------------ * FIX: Detect and apply precomputed fieldmaps (#3439) * FIX: Calculate bold mask and dummy scans in transform-only runs (#3428) * FIX: Use consistent skull-stripping pre- and post- SDC (#3415) * FIX: Use removeprefix instead of lstrip or ternary operator (#3409) * FIX: Listify sessions when generating reports (#3408) * FIX: Ensure fieldmap is resampled correctly in report (#3387) * FIX: Stop excluding FS minc_modify_header used during fallback registration (#3372) * FIX: Repair and test query for precalculated baseline/boldref files (#3370) * FIX: Repair search for precomputed transforms (#3369) * ENH: Enable Jacobians only for PEPOLAR by default, allow forcing (#3443) * ENH: Create `--force` flag that accepts a list, replacing individual `--force-*` flags (#3442) * ENH: Output fsLR meshes on subject surfaces (#3411) * ENH: Flexibilize "sophisticated" pepolar to allow monomodal execution (#3393) * ENH: Update FSL packages for reported bug fixes (#3374) * RF: Calculate RMSD from motion transforms (#3427) * RF: Reconstruct motion confounds from minimal derivatives (#3424) * RF: Replace deprecated pkgutil.find_loader (#3384) * RF: Upgrade nitransforms and remove workarounds (#3378) * DOC: Fix xfm extension in the outputs docs (#3435) * DOC: Mention fMRIPost-AROMA in parser documentation (#3356) * MNT: Remove CLI flags with expired deprecation periods (#3445) * MNT: Update pinned environment (#3440) * MNT: Bump pins, update RTD config (#3425) * MNT: Declare linux/amd64 platform during Docker build (#3422) * MNT: Bump astral-sh/setup-uv from 4 to 5 (#3417) * MNT: Test support for Python 3.13 (#3416) * MNT: Install Workbench CLI via conda (#3410) * MNT: Update minimum dependencies, test with tox-uv (#3412) * MNT: Install c3d through conda (#3382) * CI: Fetch tags and 200 commits to support describe (#3381) * CI: Build docker images in GHA, store cache inline and push to GHCR (#3380)
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‎.maint/CONTRIBUTORS.md

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@@ -13,6 +13,7 @@ Before every release, unlisted contributors will be invited again to add their n
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| Bellec | Pierre | | 0000-0002-9111-0699 | SIMEXP Lab, CRIUGM, University of Montréal, Montréal, Canada |
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| Benson | Noah C. | | 0000-0002-2365-8265 | Department of Psychology, New York University |
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| Bhagwat | Nikhil | | 0000-0001-6073-7141 | Montreal Neurological Institute, McGill University |
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| Callenberg | Keith | | 0000-0001-7786-9300 | Department of Psychiatry, University of Pittsburgh |
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| Cieslak | Matthew | | 0000-0002-1931-4734 | Perelman School of Medicine, University of Pennsylvania, PA, USA |
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| de la Vega | Alejandro | | 0000-0001-9062-3778 | University of Texas at Austin |
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| Devenyi | Grabriel A. | | 0000-0002-7766-1187 | Department of Psychiatry, McGill University |
@@ -43,6 +44,7 @@ Before every release, unlisted contributors will be invited again to add their n
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| Plunkett | Dillon | | 0000-0001-7822-6024 | Department of Psychology, Harvard University |
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| Provins | Céline | | 0000-0002-1668-9629 | Department of Radiology, Lausanne University Hospital and University of Lausanne |
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| Rivera-Dompenciel | Adriana | | 0000-0002-3339-4857 | Neuroscience Program, University of Iowa |
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| Sadil | Patrick | | 0000-0003-4141-1343 | Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, MD, USA |
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| Satterthwaite | Theodore D. | | 0000-0001-7072-9399 | Perelman School of Medicine, University of Pennsylvania, PA, USA |
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| Schaefer | Theo A.J. | | 0000-0003-4102-559X | Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany |
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| Sitek | Kevin R. | | 0000-0002-2172-5786 | Speech & Hearing Bioscience & Technology Program, Harvard University |
@@ -55,6 +57,7 @@ Before every release, unlisted contributors will be invited again to add their n
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| Valabregue | Romain | | 0000-0002-1814-9570 | CENIR, INSERM U1127, CNRS UMR 7225, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France |
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| Velasco | Pablo | | 0000-0002-5749-6049 | Center for Brain Imaging, New York University |
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| Waller | Lea | | 0000-0002-3239-6957 | Charite Universitatsmedizin Berlin, Germany |
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| Wang | Hao-Ting | | 0000-0003-4078-2038 | SIMEXP Lab, CRIUGM, University of Montréal, Montréal, Canada |
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| Wexler | Joseph B. | | 0000-0001-6424-8740 | Department of Psychology, Stanford University |
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| Wright | Jessey | | 0000-0001-5504-8579 | Department of Psychology, Stanford University |
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| Ye | Zhifang | | 0000-0003-0489-2619 | State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University |

‎.maint/update_zenodo.py

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#!/usr/bin/env python3
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# /// script
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# requires-python = ">=3.12"
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# dependencies = [
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# "fuzzywuzzy",
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# "python-levenshtein",
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# ]
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# ///
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"""Update and sort the creators list of the zenodo record."""
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import json

‎.zenodo.json

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"type": "Researcher"
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},
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{
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"affiliation": "Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń",
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"name": "Finc, Karolina",
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"orcid": "0000-0002-0157-030X",
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"affiliation": "Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, MD, USA",
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"name": "Sadil, Patrick",
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"orcid": "0000-0003-4141-1343",
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"type": "Researcher"
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},
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{
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"affiliation": "Florey Institute of Neuroscience and Mental Health",
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"name": "Smith, Robert E.",
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"orcid": "0000-0003-3636-4642",
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"affiliation": "Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń",
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"name": "Finc, Karolina",
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"orcid": "0000-0002-0157-030X",
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"type": "Researcher"
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},
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{
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"orcid": "0000-0002-6533-2909",
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"type": "Researcher"
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},
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{
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"affiliation": "Florey Institute of Neuroscience and Mental Health",
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"name": "Smith, Robert E.",
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"orcid": "0000-0003-3636-4642",
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"type": "Researcher"
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},
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{
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"affiliation": "Department of Neuroscience, University of Pennsylvania, PA, USA",
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"name": "Tooley, Ursula A.",
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"orcid": "0000-0001-6377-3885",
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"type": "Researcher"
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},
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{
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"affiliation": "Montreal Neurological Institute, McGill University",
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"name": "Bhagwat, Nikhil",
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"orcid": "0000-0001-6073-7141",
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"type": "Researcher"
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},
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{
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"affiliation": "Dartmouth College: Hanover, NH, United States",
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"name": "Halchenko, Yaroslav O.",
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"orcid": "0000-0003-3456-2493",
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"type": "Researcher"
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},
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{
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"affiliation": "Montreal Neurological Institute, McGill University",
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"name": "Bhagwat, Nikhil",
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"orcid": "0000-0001-6073-7141",
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"affiliation": "Neuro Data Science ORIGAMI Laboratory, McConnell Brain Imaging Centre, Faculty of Medicine, McGill University, Montréal, Canada",
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"name": "Gau, Rémi",
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"orcid": "0000-0002-1535-9767",
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"type": "Researcher"
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},
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{
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"type": "Researcher"
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},
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{
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"affiliation": "Neuro Data Science ORIGAMI Laboratory, McConnell Brain Imaging Centre, Faculty of Medicine, McGill University, Montréal, Canada",
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"name": "Gau, Rémi",
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"orcid": "0000-0002-1535-9767",
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"affiliation": "Department of Psychology, University of California, Berkeley",
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"name": "Lurie, Daniel J.",
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"orcid": "0000-0001-8012-6399",
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"type": "Researcher"
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},
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{
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"orcid": "0000-0001-7139-6661",
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"type": "Researcher"
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},
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{
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"affiliation": "Department of Psychology, University of California, Berkeley",
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"name": "Lurie, Daniel J.",
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"orcid": "0000-0001-8012-6399",
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"type": "Researcher"
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},
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{
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"affiliation": "Computational Neuroimaging Lab, BioCruces Health Research Institute",
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"name": "Erramuzpe, Asier",
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"orcid": "0000-0002-9402-2184",
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"type": "Researcher"
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},
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{
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"affiliation": "State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University",
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"name": "Ye, Zhifang",
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"orcid": "0000-0003-0489-2619",
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"type": "Researcher"
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},
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{
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"affiliation": "Department of Psychology, Stanford University",
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"name": "Thompson, William H.",
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"orcid": "0000-0002-0533-6035",
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"type": "Researcher"
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},
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{
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"affiliation": "Department of Psychology, Columbia University",
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"name": "Jacoby, Nir",
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"orcid": "0000-0001-7936-9991",
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"type": "Researcher"
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},
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{
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"affiliation": "Speech & Hearing Bioscience & Technology Program, Harvard University",
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"name": "Sitek, Kevin R.",
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"orcid": "0000-0002-2172-5786",
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"type": "Researcher"
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},
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{
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"affiliation": "Center for Lifespan Changes in Brain and Cognition, University of Oslo",
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"name": "Amlien, Inge K.",
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"orcid": "0000-0002-8508-9088",
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"type": "Researcher"
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},
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{
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"affiliation": "URPP Dynamics of Healthy Aging, University of Zurich",
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"name": "Liem, Franz",
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"orcid": "0000-0003-0646-4810",
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"type": "Researcher"
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},
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"affiliation": "Department of Psychology, Harvard University",
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"name": "Plunkett, Dillon",
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"orcid": "0000-0002-5740-9451",
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"type": "Researcher"
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},
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{
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"affiliation": "Department of Psychiatry, University of Pittsburgh",
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"name": "Callenberg, Keith",
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"orcid": "0000-0001-7786-9300",
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"type": "Researcher"
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},
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{
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"affiliation": "Department of Psychology, Stanford University",
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"name": "Wexler, Joseph B.",
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"orcid": "0000-0001-6424-8740",
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"type": "Researcher"
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},
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{
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"affiliation": "SIMEXP Lab, CRIUGM, University of Montréal, Montréal, Canada",
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"name": "Wang, Hao-Ting",
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"orcid": "0000-0003-4078-2038",
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"type": "Researcher"
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},
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{
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"affiliation": "Dartmouth College: Hanover, NH, United States",
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"name": "Ma, Feilong",
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"orcid": "0000-0002-6838-3971",
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"type": "Researcher"
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},
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{
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"affiliation": "Perelman School of Medicine, University of Pennsylvania, PA, USA",
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"name": "Adebimpe, Azeez",
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"orcid": "0000-0001-9049-0135",
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"affiliation": "Neuroscience Program, University of Iowa",
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"name": "Rivera-Dompenciel, Adriana",
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"orcid": "0000-0002-3339-4857",
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"type": "Researcher"
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},
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{
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"affiliation": "Center for Lifespan Changes in Brain and Cognition, University of Oslo",
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"name": "Amlien, Inge K.",
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"orcid": "0000-0002-8508-9088",
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"affiliation": "Perelman School of Medicine, University of Pennsylvania, PA, USA",
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"name": "Adebimpe, Azeez",
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"orcid": "0000-0001-9049-0135",
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"orcid": "0000-0002-1652-9297",
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"type": "Researcher"
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{
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"affiliation": "Department of Psychology, Columbia University",
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"name": "Jacoby, Nir",
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},
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"affiliation": "Department of Psychology, University of Washington",
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"name": "Kruper, John",
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"orcid": "0000-0003-0081-391X",
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},
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{
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"affiliation": "URPP Dynamics of Healthy Aging, University of Zurich",
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"name": "Liem, Franz",
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"orcid": "0000-0003-0646-4810",
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"affiliation": "Department of Psychology, Stanford University",
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"name": "Moodie, Craig A.",
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"orcid": "0000-0001-6948-9068",
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"type": "Researcher"
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{
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"affiliation": "Neuroscience Program, University of Iowa",
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"name": "Rivera-Dompenciel, Adriana",
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"orcid": "0000-0002-3339-4857",
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"type": "Researcher"
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{
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"affiliation": "Perelman School of Medicine, University of Pennsylvania, PA, USA",
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"name": "Satterthwaite, Theodore D.",
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"orcid": "0000-0001-7072-9399",
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"type": "Researcher"
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},
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{
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"affiliation": "Speech & Hearing Bioscience & Technology Program, Harvard University",
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"name": "Sitek, Kevin R.",
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"orcid": "0000-0002-2172-5786",
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"type": "Researcher"
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},
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{
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"affiliation": "Center for Lifespan Changes in Brain and Cognition, University of Oslo",
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"name": "Sneve, Markus H.",
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"orcid": "0000-0002-9699-9052",
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{
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"affiliation": "Department of Psychology, Stanford University",
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"name": "Thompson, William H.",
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"orcid": "0000-0002-0533-6035",
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},
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"affiliation": "CENIR, INSERM U1127, CNRS UMR 7225, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France",
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"name": "Valabregue, Romain",
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"orcid": "0000-0001-5504-8579",
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"type": "Researcher"
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{
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"affiliation": "State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University",
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"name": "Ye, Zhifang",
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"orcid": "0000-0003-0489-2619",
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"type": "Researcher"
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},
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{
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"affiliation": "McGovern Institute for Brain Research, MIT, MA, USA",
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"name": "Ghosh, Satrajit S.",

‎CHANGES.rst

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24.1.2 (To be determined)
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=========================
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Bug fix release in the 24.1.x series.
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25.0.0 (March 25, 2025)
2+
=======================
3+
New feature release in the 25.0.x series.
4+
5+
This release substantially improves support for pre-computed derivatives.
6+
Previous releases would miss some derivatives and rerun the computations.
7+
Note that derivatives from previous versions will be accepted,
8+
so it should not be necessary to recompute derivatives from previous versions.
9+
The recommended command line is::
10+
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fmriprep BIDS_DIR OUT_DIR participant --derivatives fmriprep=PRECOMP_DIR
12+
13+
Note that multiple derivatives can be specified, for example::
14+
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fmriprep BIDS_DIR OUT_DIR participant \
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anat=PRECOMPUTED_ANATOMICAL_DIR \
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func=PRECOMPUTED_FUNCTIONAL_DIR
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When the same file is found in multiple derivatives, the last one found takes precedence.
20+
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Additionally, `--force-*` flags have been consolidated into a single
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`--force` flag that can take multiple, space-separated arguments.
423

24+
Structural processing changes
25+
-----------------------------
26+
We now output white, pial and midthickness fsLR meshes on the subject surface.
27+
Look for `sub-<subject>_hemi-<L|R>_space-fsLR_*_<surf>.surf.gii` files.
28+
29+
Brain extraction has been modified slightly to more closely match the
30+
`antsBrainExtraction.sh` workflow distributed by ANTs.
31+
The impact should be minimal, but in rare cases this fixes a crash.
32+
33+
Fieldmap processing changes
34+
---------------------------
35+
SyN-SDC fieldmap filtering is now single-level, following the improvements
36+
for gradient-echo fieldmaps in 24.1.
37+
38+
Jacobian-weighting during fieldmap unwarping is now on by default *only*
39+
for PEPolar fieldmaps.
40+
To enable for other fieldmap types, use `--force fieldmap-jacobian`.
41+
42+
All merged pull requests
43+
------------------------
44+
45+
* FIX: Detect and apply precomputed fieldmaps (#3439)
46+
* FIX: Calculate bold mask and dummy scans in transform-only runs (#3428)
47+
* FIX: Use consistent skull-stripping pre- and post- SDC (#3415)
48+
* FIX: Use removeprefix instead of lstrip or ternary operator (#3409)
49+
* FIX: Listify sessions when generating reports (#3408)
550
* FIX: Ensure fieldmap is resampled correctly in report (#3387)
51+
* FIX: Stop excluding FS minc_modify_header used during fallback registration (#3372)
52+
* FIX: Repair and test query for precalculated baseline/boldref files (#3370)
53+
* FIX: Repair search for precomputed transforms (#3369)
54+
* ENH: Enable Jacobians only for PEPOLAR by default, allow forcing (#3443)
55+
* ENH: Create `--force` flag that accepts a list, replacing individual `--force-*` flags (#3442)
56+
* ENH: Output fsLR meshes on subject surfaces (#3411)
57+
* ENH: Flexibilize "sophisticated" pepolar to allow monomodal execution (#3393)
58+
* ENH: Update FSL packages for reported bug fixes (#3374)
59+
* RF: Calculate RMSD from motion transforms (#3427)
60+
* RF: Reconstruct motion confounds from minimal derivatives (#3424)
61+
* RF: Replace deprecated pkgutil.find_loader (#3384)
62+
* RF: Upgrade nitransforms and remove workarounds (#3378)
63+
* DOC: Fix xfm extension in the outputs docs (#3435)
64+
* DOC: Mention fMRIPost-AROMA in parser documentation (#3356)
65+
* MNT: Remove CLI flags with expired deprecation periods (#3445)
66+
* MNT: Update pinned environment (#3440)
67+
* MNT: Bump pins, update RTD config (#3425)
68+
* MNT: Declare linux/amd64 platform during Docker build (#3422)
69+
* MNT: Bump astral-sh/setup-uv from 4 to 5 (#3417)
70+
* MNT: Test support for Python 3.13 (#3416)
71+
* MNT: Install Workbench CLI via conda (#3410)
72+
* MNT: Update minimum dependencies, test with tox-uv (#3412)
73+
* MNT: Install c3d through conda (#3382)
74+
* CI: Fetch tags and 200 commits to support describe (#3381)
75+
* CI: Build docker images in GHA, store cache inline and push to GHCR (#3380)
676

777

878
24.1.1 (October 10, 2024)

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