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Merge tag '2.13.0'
2.13.0 (May 15, 2025) Feature release in the 2.13.x series. This release addresses some longstanding issues with the SyN-SDC workflow, improving the registration quality in adult humans by utilizing a spatial prior, as well as allowing Laplacians to be up- or down-weighted in the cost function, making it more usable across species. Additionally, this release allows for the use of ``EstimatedTotalReadoutTime`` or ``EstimatedEchoSpacing``, or a manually provided fallback ``TotalReadoutTime`` value, permitting the use of SDCFlows on datasets that do not have reliable timing information without introducing incorrect metadata into the datasets. * fix(syn): Re-enable priors respecting ``sd_priors`` argument (#488) * feat: Add workflow arguments for metadata estimates and fallback TRT (#479) * feat(syn): Update totalFieldVarianceInVoxel space based on voxel resolution (#487) * feat(syn): Allow changing laplacians weights in SyN registration metric (#484) * test(syn): Add a test to exercise SyN workflow creation and check parameters (#486)
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‎.github/workflows/docs-build-update.yml‎

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on:
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push:
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branches: [ 'doc/*', 'docs/*', master, "maint/*" ]
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branches: [ 'doc/*', 'docs/*', master, main, "maint/*" ]
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tags: [ '*' ]
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pull_request:
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branches: [ master, 'maint/*' ]
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branches: [ master, main, 'maint/*' ]
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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git push
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- name: Push "master" docs to gh-pages after a push to master (typically, a PR merge).
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if: github.ref == 'refs/heads/master'
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if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main'
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run: |
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if [[ "${CURBRANCH}" != "master" ]]; then
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if [[ "${CURBRANCH}" != "master" -a "${CURBRANCH}" != "main" ]]; then
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echo "$CURBRANCH is not the default development branch"
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exit 1
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fi
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git checkout -b gh-pages origin/gh-pages
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git rm -r master/ || true
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git rm -r ${CURBRANCH}/ || true
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# It is fundamental that the directory does not exist at all.
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rm -rf master
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cp -r $HOME/docs/$CURBRANCH $PWD/master
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git add master
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git commit -am "docs(master): Update docs of development line" || true
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rm -rf ${CURBRANCH}
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cp -r $HOME/docs/$CURBRANCH $PWD/${CURBRANCH}
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git add ${CURBRANCH}
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git commit -am "docs(${CURBRANCH}): Update docs of development line" || true
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git push

‎.mailmap‎

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@@ -38,15 +38,18 @@ Krzysztof J. Gorgolewski <[email protected]> <filo@filo-Precision-
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Krzysztof J. Gorgolewski <[email protected]> <filo@filo-Precision-M6500>
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Krzysztof J. Gorgolewski <[email protected]> <filo@filolaptop>
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Krzysztof J. Gorgolewski <[email protected]> <[email protected]>
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Lea Waller <[email protected]> <[email protected]>
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Marc Bue <[email protected]>
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Markus H. Sneve <[email protected]> <[email protected]>
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Mathias Goncalves <[email protected]>
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Mathias Goncalves <[email protected]> <[email protected]>
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Mathias Goncalves <[email protected]> <[email protected]>
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Mathieu Dugré <[email protected]>
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Matteo Visconti di Oleggio Castello <[email protected]>
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Marc Bue <[email protected]>
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Marc Bue <[email protected]> marcbue <[email protected]>
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Mikael Naveau <[email protected]>
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Milton Camacho <[email protected]>
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Nir Jacoby <[email protected]>
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Nir Jacoby <[email protected]> <[email protected]>
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Noah C. Benson <[email protected]>
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Soichi Hayashi <[email protected]>
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William Hedley Thompson <[email protected]>
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William Hedley Thompson <[email protected]> <[email protected]>
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Yasser Aleman <[email protected]>

‎.maint/CONTRIBUTORS.md‎

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| **Lastname** | **Name** | **Handle** | **ORCID** | **Affiliation** |
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| --- | --- | --- | --- | --- |
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| Adebimpe | Azeez | @a3sha2 | 0000-0001-9049-0135 | Perelman School of Medicine, University of Pennsylvania, PA, USA |
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| Aleman | Yasser | @yasseraleman | | |
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| Blair | Ross W. | @rwblair | 0000-0003-3007-1056 | Department of Psychology, Stanford University, CA, USA |
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| Camacho | Milton | @miltoncamacho | | |
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| Cieslak | Matthew | @mattcieslak | 0000-0002-1931-4734 | Perelman School of Medicine, University of Pennsylvania, PA, USA |
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| Dugré | Mathieu | @mathdugre | 0000-0003-2828-6031 | Concordia University |
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| Legarreta Gorroño | Jon Haitz | @jhlegarreta | 0000-0002-9661-1396 | Brigham and Women's Hospital, Mass General Brigham, Harvard Medical School, MA, USA |
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| MacNicol | Eilidh | @eilidhmacnicol | 0000-0003-3715-7012 | Department of Neuroimaging, King's College London |
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| Marabotto | Julien | @jmarabotto | 0009-0003-7070-5217 | Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland |
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| Meisler | Steven | @smeisler | 0000-0002-8888-1572 | Speech & Hearing Bioscience & Technology Program, Harvard University |
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| Naveau | Mikaël | @naveau | 0000-0001-6948-9068 | Cyceron, UMS 3408 (CNRS - UCBN), France |
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| Pinsard | Basile | @bpinsard | 0000-0002-4391-3075 | University of Montréal, Montréal, Canada |
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| Sadil | Patrick | @psadil | 0000-0003-4141-1343 | Johns Hopkins Bloomberg School of Public Health |
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| Salo | Taylor | @tsalo | 0000-0001-9813-3167 | Perelman School of Medicine, University of Pennsylvania, PA, USA |
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| Sitek | Kevin R. | @sitek | 0000-0002-2172-5786 | Speech & Hearing Bioscience & Technology Program, Harvard University |
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| Sneve | Markus H. | @markushs | 0000-0001-7644-7915 | Center for Lifespan Changes in Brain and Cognition, University of Oslo |
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| Waller | Lea | @hippocampusgirl | 0000-0002-3239-6957 | Charite Universitatsmedizin Berlin, Germany |
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| Zwiers | Marcel | @marcelzwiers | | |

‎.maint/update_authors.py‎

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#!/usr/bin/env python3
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# /// script
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# requires-python = ">=3.13"
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# dependencies = [
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# "click",
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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 sys
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from pathlib import Path

‎.zenodo.json‎

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],
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"contributors": [
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{
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"orcid": "0000-0003-3007-1056",
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"affiliation": "Department of Psychology, Stanford University, CA, USA",
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"name": "Ross W. Blair",
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"orcid": "0009-0003-7070-5217",
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"affiliation": "Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland",
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"name": "Julien Marabotto",
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"type": "Researcher"
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},
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{
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"orcid": "0000-0002-4391-3075",
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"affiliation": "University of Montréal, Montréal, Canada",
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"name": "Basile Pinsard",
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"type": "Researcher"
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},
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{
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"name": "Taylor Salo",
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"type": "Researcher"
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},
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{
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"orcid": "0000-0003-4141-1343",
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"affiliation": "Johns Hopkins Bloomberg School of Public Health",
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"name": "Patrick Sadil",
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"type": "Researcher"
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},
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{
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"orcid": "0000-0003-2828-6031",
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"affiliation": "Concordia University",
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"name": "Mathieu Dugré",
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"type": "Researcher"
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},
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{
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"orcid": "0000-0003-3715-7012",
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"affiliation": "Department of Neuroimaging, King's College London",
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"name": "Eilidh MacNicol",
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"type": "Researcher"
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},
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{
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"orcid": "0000-0002-1931-4734",
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"affiliation": "Perelman School of Medicine, University of Pennsylvania, PA, USA",
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"name": "Matthew Cieslak",
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"type": "Researcher"
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"name": "Marcel Zwiers",
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"type": "Researcher",
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"affiliation": "Unknown affiliation"
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},
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{
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"name": "Yasser Aleman",
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"type": "Researcher",
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"affiliation": "Unknown affiliation"
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},
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{
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"orcid": "0000-0002-8888-1572",
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"type": "Researcher"
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},
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{
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"orcid": "0000-0002-4391-3075",
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"affiliation": "University of Montréal, Montréal, Canada",
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"name": "Basile Pinsard",
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"orcid": "0000-0002-3239-6957",
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"affiliation": "Charite Universitatsmedizin Berlin, Germany",
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"name": "Lea Waller",
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"type": "Researcher"
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},
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{
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"name": "Milton Camacho",
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"type": "Researcher",
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"affiliation": "Unknown affiliation"
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},
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{
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"orcid": "0000-0002-9661-1396",
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"affiliation": "Brigham and Women's Hospital, Mass General Brigham, Harvard Medical School, MA, USA",
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"name": "Jon Haitz Legarreta Gorroño",
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"type": "Researcher"
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},
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{
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"orcid": "0000-0001-9049-0135",
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"affiliation": "Perelman School of Medicine, University of Pennsylvania, PA, USA",
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"name": "Azeez Adebimpe",
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"type": "Researcher"
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},
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{
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"name": "Markus H. Sneve",
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"type": "Researcher"
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},
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{
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"orcid": "0000-0002-1931-4734",
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"affiliation": "Perelman School of Medicine, University of Pennsylvania, PA, USA",
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"name": "Matthew Cieslak",
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"type": "Researcher"
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},
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{
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"orcid": "0000-0001-6948-9068",
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"affiliation": "Cyceron, UMS 3408 (CNRS - UCBN), France",
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"name": "Mikaël Naveau",
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"type": "Researcher"
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},
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{
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"orcid": "0000-0001-9049-0135",
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"affiliation": "Perelman School of Medicine, University of Pennsylvania, PA, USA",
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"name": "Azeez Adebimpe",
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"orcid": "0000-0003-3007-1056",
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"affiliation": "Department of Psychology, Stanford University, CA, USA",
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"name": "Ross W. Blair",
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"type": "Researcher"
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},
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{

‎CHANGES.rst‎

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2.13.0 (May 15, 2025)
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=====================
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Feature release in the 2.13.x series.
4+
5+
This release addresses some longstanding issues with the SyN-SDC workflow,
6+
improving the registration quality in adult humans by utilizing a spatial prior,
7+
as well as allowing Laplacians to be up- or down-weighted in the cost function,
8+
making it more usable across species.
9+
10+
Additionally, this release allows for the use of ``EstimatedTotalReadoutTime`` or
11+
``EstimatedEchoSpacing``, or a manually provided fallback ``TotalReadoutTime`` value,
12+
permitting the use of SDCFlows on datasets that do not have reliable timing information
13+
without introducing incorrect metadata into the datasets.
14+
15+
* fix(syn): Re-enable priors respecting ``sd_priors`` argument (#488)
16+
* feat: Add workflow arguments for metadata estimates and fallback TRT (#479)
17+
* feat(syn): Update totalFieldVarianceInVoxel space based on voxel resolution (#487)
18+
* feat(syn): Allow changing laplacians weights in SyN registration metric (#484)
19+
* test(syn): Add a test to exercise SyN workflow creation and check parameters (#486)
20+
21+
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2.12.0 (March 21, 2025)
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=======================
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Feature release in the 2.12.x series.

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