REL: 2.13.0

.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

.mailmap

@@ -38,15 +38,18 @@ Krzysztof J. Gorgolewski <krzysztof.gorgolewski@gmail.com> <filo@filo-Precision-
 Krzysztof J. Gorgolewski <krzysztof.gorgolewski@gmail.com> <filo@filo-Precision-M6500>
 Krzysztof J. Gorgolewski <krzysztof.gorgolewski@gmail.com> <filo@filolaptop>
 Krzysztof J. Gorgolewski <krzysztof.gorgolewski@gmail.com> <krzysztof.gorgolewski+fake@gmail.com>
+Lea Waller <lea.waller@charite.de> <lea@lea.science>
 Marc Bue <44844855+marcbue@users.noreply.github.com>
 Markus H. Sneve <m.h.sneve@psykologi.uio.no> <44242647+markushs@users.noreply.github.com>
 Mathias Goncalves <goncalves.mathias@gmail.com>
 Mathias Goncalves <goncalves.mathias@gmail.com> <mathiasg@mit.edu>
 Mathias Goncalves <goncalves.mathias@gmail.com> <mathiasg@stanford.edu>
+Mathieu Dugré <16450132+mathdugre@users.noreply.github.com>
 Matteo Visconti di Oleggio Castello <matteo.visconti.gr@dartmouth.edu>
 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 <naveau.mikael@gmail.com>
+Milton Camacho <70858549+miltoncamacho@users.noreply.github.com>
 Nir Jacoby <nj2319@columbia.edu>
 Nir Jacoby <nj2319@columbia.edu> <nirjacoby@dyn-128-59-231-222.dyn.columbia.edu>
 Noah C. Benson <nben@nyu.edu>
@@ -67,3 +70,4 @@ Shoshana Berleant <berleant@stanford.edu>  <shoshber@users.noreply.github.com>
 Soichi Hayashi <hayashis@iu.edu>
 William Hedley Thompson <william.thompson@ki.se>
 William Hedley Thompson <william.thompson@ki.se> <wiheto@users.noreply.github.com>
+Yasser Aleman <yasseraleman@gmail.com>

.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 |  |  |

.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

.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"
     },
     {
@@ -31,17 +37,33 @@
       "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",
       "name": "Eilidh MacNicol",
       "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"
     },
     {
@@ -67,16 +106,22 @@
       "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",
       "name": "Mikaël Naveau",
       "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"
     },
     {

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.