Merge tag '24.1.0'

24.1.0 (September 16, 2024)

New feature release in the 24.1.x series.

Handling of gradient echo fieldmaps is improved.

  * FIX: Select volumetric dseg.tsv from recent TemplateFlow releases (#3257)
  * RF: Adapt to less T1w-centric smriprep (#3333)
  * RF: Use acres over vendored data loader (#3323)
  * DOC: Add benchmark page (#3312)
  * MAINT: Move to tox to simplify test/CI setup (#3326)
  * CI: Fix expected outputs for fieldmaps (#3321)

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ repos:
       - id: check-toml
       - id: check-added-large-files
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.3
+    rev: v0.6.2
     hooks:
       - id: ruff
         args: [ --fix ]

CHANGES.rst

@@ -1,3 +1,16 @@
+24.1.0 (September 16, 2024)
+===========================
+New feature release in the 24.1.x series.
+
+Handling of gradient echo fieldmaps is improved.
+
+  * FIX: Select volumetric dseg.tsv from recent TemplateFlow releases (#3257)
+  * RF: Adapt to less T1w-centric smriprep (#3333)
+  * RF: Use acres over vendored data loader (#3323)
+  * DOC: Add benchmark page (#3312)
+  * MAINT: Move to tox to simplify test/CI setup (#3326)
+  * CI: Fix expected outputs for fieldmaps (#3321)
+
 24.0.1 (July 16, 2024)
 ======================
 Bug fix release in the 24.0.x series.

Dockerfile

@@ -40,7 +40,7 @@ RUN python -m build /src
 #
 
 # Utilities for downloading packages
-FROM ${BASE_IMAGE} as downloader
+FROM ${BASE_IMAGE} AS downloader
 # Bump the date to current to refresh curl/certificates/etc
 RUN echo "2023.07.20"
 RUN apt-get update && \
@@ -53,13 +53,13 @@ RUN apt-get update && \
     apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 # FreeSurfer 7.3.2
-FROM downloader as freesurfer
+FROM downloader AS freesurfer
 COPY docker/files/freesurfer7.3.2-exclude.txt /usr/local/etc/freesurfer7.3.2-exclude.txt
 RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer-linux-ubuntu22_amd64-7.3.2.tar.gz \
      | tar zxv --no-same-owner -C /opt --exclude-from=/usr/local/etc/freesurfer7.3.2-exclude.txt
 
 # AFNI
-FROM downloader as afni
+FROM downloader AS afni
 # Bump the date to current to update AFNI
 RUN echo "2023.07.20"
 RUN mkdir -p /opt/afni-latest \
@@ -80,7 +80,7 @@ RUN mkdir -p /opt/afni-latest \
         -name "3dvolreg" \) -delete
 
 # Connectome Workbench 1.5.0
-FROM downloader as workbench
+FROM downloader AS workbench
 RUN mkdir /opt/workbench && \
     curl -sSLO https://www.humanconnectome.org/storage/app/media/workbench/workbench-linux64-v1.5.0.zip && \
     unzip workbench-linux64-v1.5.0.zip -d /opt && \
@@ -89,13 +89,13 @@ RUN mkdir /opt/workbench && \
     strip --remove-section=.note.ABI-tag /opt/workbench/libs_linux64/libQt5Core.so.5
 
 # Convert3d 1.4.0
-FROM downloader as c3d
+FROM downloader AS c3d
 RUN mkdir /opt/convert3d && \
     curl -fsSL --retry 5 https://sourceforge.net/projects/c3d/files/c3d/Experimental/c3d-1.4.0-Linux-gcc64.tar.gz/download \
     | tar -xz -C /opt/convert3d --strip-components 1
 
 # Micromamba
-FROM downloader as micromamba
+FROM downloader AS micromamba
 
 # Install a C compiler to build extensions when needed.
 # traits<6.4 wheels are not available for Python 3.11+, but build easily.
@@ -119,13 +119,13 @@ RUN micromamba create -y -f /tmp/env.yml && \
 # Check if this is still necessary when updating the base image.
 ENV PATH="/opt/conda/envs/fmriprep/bin:$PATH" \
     UV_USE_IO_URING=0
-RUN npm install -g svgo@^3.2.0 bids-validator@^1.14.0 && \
+RUN npm install -g svgo@^3.2.0 bids-validator@1.14.10 && \
     rm -r ~/.npm
 
 #
 # Main stage
 #
-FROM ${BASE_IMAGE} as fmriprep
+FROM ${BASE_IMAGE} AS fmriprep
 
 # Configure apt
 ENV DEBIAN_FRONTEND="noninteractive" \

env.yml

@@ -15,12 +15,12 @@ dependencies:
   # Base scientific python stack; required by FSL, so pinned here
   - numpy=1.26
   - scipy=1.13
-  - matplotlib=3.8
+  - matplotlib=3.9
   - pandas=2.2
   - h5py=3.11
   # Dependencies compiled against numpy, best to stick with conda
   - nitime=0.10
-  - scikit-image=0.23
+  - scikit-image=0.24
   - scikit-learn=1.4
   # Utilities
   - graphviz=9.0

fmriprep/workflows/bold/resampling.py

@@ -575,10 +575,10 @@ def init_bold_fsLR_resampling_wf(
         Path to BOLD series resampled as functional GIFTI files in fsLR space
 
     """
+    import smriprep.data
     import templateflow.api as tf
     from niworkflows.engine.workflows import LiterateWorkflow as Workflow
     from niworkflows.interfaces.utility import KeySelect
-    from smriprep import data as smriprep_data
 
     from fmriprep.interfaces.workbench import VolumeToSurfaceMapping
 
@@ -652,7 +652,7 @@ def init_bold_fsLR_resampling_wf(
             extension='.surf.gii',
         )
     ]
-    atlases = smriprep_data.load_resource('atlases')
+    atlases = smriprep.data.load('atlases')
     select_surfaces.inputs.template_roi = [
         str(atlases / f'L.atlasroi.{fslr_density}_fs_LR.shape.gii'),
         str(atlases / f'R.atlasroi.{fslr_density}_fs_LR.shape.gii'),

pyproject.toml

@@ -23,18 +23,18 @@ dependencies = [
     "looseversion",
     "nibabel >= 4.0.1",
     "nipype >= 1.8.5",
-    "nireports @ git+https://github.com/nipreps/nireports.git@main",
+    "nireports >= 23.2.2",
     "nitime",
-    "nitransforms >= 21.0.0",
-    "niworkflows @ git+https://github.com/nipreps/niworkflows.git@master",
+    "nitransforms >= 21.0.0, != 24.0.0",
+    "niworkflows >= 1.11.0",
     "numpy >= 1.22",
     "packaging",
     "pandas",
     "psutil >= 5.4",
     "pybids >= 0.15.2",
     "requests",
-    "sdcflows @ git+https://github.com/nipreps/sdcflows.git@master",
-    "smriprep @ git+https://github.com/nipreps/smriprep.git@master",
+    "sdcflows >= 2.10.0",
+    "smriprep >= 0.16.0",
     "tedana >= 23.0.2",
     "templateflow >= 24.1.0",
     "transforms3d",