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REL: 24.1.0 #3353

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Sep 16, 2024
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2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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 ]
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13 changes: 13 additions & 0 deletions CHANGES.rst
Original file line number Diff line number Diff line change
@@ -1,3 +1,16 @@
24.1.0 (To be Determined)
=========================
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.
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16 changes: 8 additions & 8 deletions Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -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 && \
Expand All @@ -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 \
Expand All @@ -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 && \
Expand All @@ -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.
Expand All @@ -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 [email protected].10 && \
rm -r ~/.npm

#
# Main stage
#
FROM ${BASE_IMAGE} as fmriprep
FROM ${BASE_IMAGE} AS fmriprep

# Configure apt
ENV DEBIAN_FRONTEND="noninteractive" \
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4 changes: 2 additions & 2 deletions env.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion fmriprep/conftest.py
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ def _populate_namespace(doctest_namespace, tmp_path):
doctest_namespace['testdir'] = tmp_path


@pytest.fixture()
@pytest.fixture
def minimal_bids(tmp_path):
bids = tmp_path / 'bids'
bids.mkdir()
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4 changes: 2 additions & 2 deletions fmriprep/workflows/bold/resampling.py
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -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'),
Expand Down
10 changes: 5 additions & 5 deletions pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down
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