diff --git a/.github/workflows/docs-build-update.yml b/.github/workflows/docs-build-update.yml index 6b05f0e947..4bfa0555d7 100644 --- a/.github/workflows/docs-build-update.yml +++ b/.github/workflows/docs-build-update.yml @@ -3,10 +3,10 @@ name: Build & update docs on: push: - branches: [ 'doc/*', 'docs/*', master, "maint/*" ] + branches: [ 'doc/*', 'docs/*', master, main, "maint/*" ] tags: [ '*' ] pull_request: - branches: [ master, 'maint/*' ] + branches: [ master, main, 'maint/*' ] concurrency: group: ${{ github.workflow }}-${{ github.ref }} @@ -92,17 +92,17 @@ jobs: git push - name: Push "master" docs to gh-pages after a push to master (typically, a PR merge). - if: github.ref == 'refs/heads/master' + if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' run: | - if [[ "${CURBRANCH}" != "master" ]]; then + if [[ "${CURBRANCH}" != "master" -a "${CURBRANCH}" != "main" ]]; then echo "$CURBRANCH is not the default development branch" exit 1 fi git checkout -b gh-pages origin/gh-pages - git rm -r master/ || true + git rm -r ${CURBRANCH}/ || true # It is fundamental that the directory does not exist at all. - rm -rf master - cp -r $HOME/docs/$CURBRANCH $PWD/master - git add master - git commit -am "docs(master): Update docs of development line" || true + rm -rf ${CURBRANCH} + cp -r $HOME/docs/$CURBRANCH $PWD/${CURBRANCH} + git add ${CURBRANCH} + git commit -am "docs(${CURBRANCH}): Update docs of development line" || true git push diff --git a/.mailmap b/.mailmap index 0395608ff6..a72c25b5b9 100644 --- a/.mailmap +++ b/.mailmap @@ -38,15 +38,18 @@ Krzysztof J. Gorgolewski Krzysztof J. Gorgolewski Krzysztof J. Gorgolewski +Lea Waller Marc Bue <44844855+marcbue@users.noreply.github.com> Markus H. Sneve <44242647+markushs@users.noreply.github.com> Mathias Goncalves Mathias Goncalves Mathias Goncalves +Mathieu Dugré <16450132+mathdugre@users.noreply.github.com> Matteo Visconti di Oleggio Castello Marc Bue <44844855+marcbue@users.noreply.github.com> Marc Bue <44844855+marcbue@users.noreply.github.com> marcbue <44844855+marcbue@users.noreply.github.com> Mikael Naveau +Milton Camacho <70858549+miltoncamacho@users.noreply.github.com> Nir Jacoby Nir Jacoby Noah C. Benson @@ -67,3 +70,4 @@ Shoshana Berleant Soichi Hayashi William Hedley Thompson William Hedley Thompson +Yasser Aleman diff --git a/.maint/CONTRIBUTORS.md b/.maint/CONTRIBUTORS.md index 55bb6aca96..42382d16c5 100644 --- a/.maint/CONTRIBUTORS.md +++ b/.maint/CONTRIBUTORS.md @@ -9,12 +9,20 @@ Before every release, unlisted contributors will be invited again to add their n | **Lastname** | **Name** | **Handle** | **ORCID** | **Affiliation** | | --- | --- | --- | --- | --- | | Adebimpe | Azeez | @a3sha2 | 0000-0001-9049-0135 | Perelman School of Medicine, University of Pennsylvania, PA, USA | +| Aleman | Yasser | @yasseraleman | | | | Blair | Ross W. | @rwblair | 0000-0003-3007-1056 | Department of Psychology, Stanford University, CA, USA | +| Camacho | Milton | @miltoncamacho | | | | Cieslak | Matthew | @mattcieslak | 0000-0002-1931-4734 | Perelman School of Medicine, University of Pennsylvania, PA, USA | +| Dugré | Mathieu | @mathdugre | 0000-0003-2828-6031 | Concordia University | +| Legarreta Gorroño | Jon Haitz | @jhlegarreta | 0000-0002-9661-1396 | Brigham and Women's Hospital, Mass General Brigham, Harvard Medical School, MA, USA | | MacNicol | Eilidh | @eilidhmacnicol | 0000-0003-3715-7012 | Department of Neuroimaging, King's College London | +| Marabotto | Julien | @jmarabotto | 0009-0003-7070-5217 | Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland | | Meisler | Steven | @smeisler | 0000-0002-8888-1572 | Speech & Hearing Bioscience & Technology Program, Harvard University | | Naveau | Mikaël | @naveau | 0000-0001-6948-9068 | Cyceron, UMS 3408 (CNRS - UCBN), France | | Pinsard | Basile | @bpinsard | 0000-0002-4391-3075 | University of Montréal, Montréal, Canada | +| Sadil | Patrick | @psadil | 0000-0003-4141-1343 | Johns Hopkins Bloomberg School of Public Health | | Salo | Taylor | @tsalo | 0000-0001-9813-3167 | Perelman School of Medicine, University of Pennsylvania, PA, USA | | Sitek | Kevin R. | @sitek | 0000-0002-2172-5786 | Speech & Hearing Bioscience & Technology Program, Harvard University | | Sneve | Markus H. | @markushs | 0000-0001-7644-7915 | Center for Lifespan Changes in Brain and Cognition, University of Oslo | +| Waller | Lea | @hippocampusgirl | 0000-0002-3239-6957 | Charite Universitatsmedizin Berlin, Germany | +| Zwiers | Marcel | @marcelzwiers | | | diff --git a/.maint/update_authors.py b/.maint/update_authors.py index 169321eb7e..0ca78d4993 100644 --- a/.maint/update_authors.py +++ b/.maint/update_authors.py @@ -1,4 +1,12 @@ #!/usr/bin/env python3 +# /// script +# requires-python = ">=3.13" +# dependencies = [ +# "click", +# "fuzzywuzzy", +# "python-levenshtein", +# ] +# /// """Update and sort the creators list of the zenodo record.""" import sys from pathlib import Path diff --git a/.zenodo.json b/.zenodo.json index 65e9fd8803..9894144510 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -20,9 +20,15 @@ ], "contributors": [ { - "orcid": "0000-0003-3007-1056", - "affiliation": "Department of Psychology, Stanford University, CA, USA", - "name": "Ross W. Blair", + "orcid": "0009-0003-7070-5217", + "affiliation": "Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland", + "name": "Julien Marabotto", + "type": "Researcher" + }, + { + "orcid": "0000-0002-4391-3075", + "affiliation": "University of Montréal, Montréal, Canada", + "name": "Basile Pinsard", "type": "Researcher" }, { @@ -31,6 +37,18 @@ "name": "Taylor Salo", "type": "Researcher" }, + { + "orcid": "0000-0003-4141-1343", + "affiliation": "Johns Hopkins Bloomberg School of Public Health", + "name": "Patrick Sadil", + "type": "Researcher" + }, + { + "orcid": "0000-0003-2828-6031", + "affiliation": "Concordia University", + "name": "Mathieu Dugré", + "type": "Researcher" + }, { "orcid": "0000-0003-3715-7012", "affiliation": "Department of Neuroimaging, King's College London", @@ -38,10 +56,14 @@ "type": "Researcher" }, { - "orcid": "0000-0002-1931-4734", - "affiliation": "Perelman School of Medicine, University of Pennsylvania, PA, USA", - "name": "Matthew Cieslak", - "type": "Researcher" + "name": "Marcel Zwiers", + "type": "Researcher", + "affiliation": "Unknown affiliation" + }, + { + "name": "Yasser Aleman", + "type": "Researcher", + "affiliation": "Unknown affiliation" }, { "orcid": "0000-0002-8888-1572", @@ -50,9 +72,26 @@ "type": "Researcher" }, { - "orcid": "0000-0002-4391-3075", - "affiliation": "University of Montréal, Montréal, Canada", - "name": "Basile Pinsard", + "orcid": "0000-0002-3239-6957", + "affiliation": "Charite Universitatsmedizin Berlin, Germany", + "name": "Lea Waller", + "type": "Researcher" + }, + { + "name": "Milton Camacho", + "type": "Researcher", + "affiliation": "Unknown affiliation" + }, + { + "orcid": "0000-0002-9661-1396", + "affiliation": "Brigham and Women's Hospital, Mass General Brigham, Harvard Medical School, MA, USA", + "name": "Jon Haitz Legarreta Gorroño", + "type": "Researcher" + }, + { + "orcid": "0000-0001-9049-0135", + "affiliation": "Perelman School of Medicine, University of Pennsylvania, PA, USA", + "name": "Azeez Adebimpe", "type": "Researcher" }, { @@ -67,6 +106,12 @@ "name": "Markus H. Sneve", "type": "Researcher" }, + { + "orcid": "0000-0002-1931-4734", + "affiliation": "Perelman School of Medicine, University of Pennsylvania, PA, USA", + "name": "Matthew Cieslak", + "type": "Researcher" + }, { "orcid": "0000-0001-6948-9068", "affiliation": "Cyceron, UMS 3408 (CNRS - UCBN), France", @@ -74,9 +119,9 @@ "type": "Researcher" }, { - "orcid": "0000-0001-9049-0135", - "affiliation": "Perelman School of Medicine, University of Pennsylvania, PA, USA", - "name": "Azeez Adebimpe", + "orcid": "0000-0003-3007-1056", + "affiliation": "Department of Psychology, Stanford University, CA, USA", + "name": "Ross W. Blair", "type": "Researcher" }, { diff --git a/CHANGES.rst b/CHANGES.rst index 7136988928..f50a296a90 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -1,3 +1,24 @@ +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) + + 2.12.0 (March 21, 2025) ======================= Feature release in the 2.12.x series.