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Revert "chore: Use pixi to manage test environment"
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‎.dockerignore‎

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@@ -12,7 +12,3 @@ fmriprep.egg-info/**/*
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fmriprep.egg-info
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.eggs/**/*
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.eggs
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.venv
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.pixi
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.tox

‎Dockerfile‎

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# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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# SOFTWARE.
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ARG BASE_IMAGE=ghcr.io/nipreps/fmriprep-base:20251006
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# Ubuntu 22.04 LTS - Jammy
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ARG BASE_IMAGE=ubuntu:jammy-20240125
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#
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# Build pixi environment
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# The Pixi environment includes:
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# - Python
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# - Scientific Python stack (via conda-forge)
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# - General Python dependencies (via PyPI)
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# - FSL (via fslconda)
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# - ants (via conda-forge)
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# - connectome-workbench (via conda-forge)
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# - ...
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# Build wheel
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#
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FROM ghcr.io/prefix-dev/pixi:0.53.0 AS build
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FROM python:slim AS src
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RUN pip install build
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RUN apt-get update && \
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apt-get install -y --no-install-recommends git
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COPY . /src
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RUN python -m build /src
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#
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# Download stages
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#
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# Utilities for downloading packages
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FROM ${BASE_IMAGE} as downloader
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# Bump the date to current to refresh curl/certificates/etc
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RUN echo "2024.03.08"
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RUN apt-get update && \
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apt-get install -y --no-install-recommends \
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binutils \
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bzip2 \
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ca-certificates \
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git && \
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curl \
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unzip && \
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apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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# Run post-link scripts during install, but use global to keep out of source tree
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RUN pixi config set --global run-post-link-scripts insecure
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# Install dependencies before the package itself to leverage caching
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RUN mkdir /app
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COPY pixi.lock pyproject.toml /app
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WORKDIR /app
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RUN --mount=type=cache,target=/root/.cache/rattler pixi install -e niworkflows -e test --frozen --skip niworkflows
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# Note that PATH gets hard-coded. Remove it and re-apply in final image
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RUN pixi shell-hook -e niworkflows --as-is | grep -v PATH > /shell-hook.sh
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RUN pixi shell-hook -e test --as-is | grep -v PATH > /test-shell-hook.sh
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# Finally, install the package
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COPY . /app
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RUN --mount=type=cache,target=/root/.cache/rattler pixi install -e niworkflows -e test --frozen
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#
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# Pre-fetch templates
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#
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FROM ghcr.io/astral-sh/uv:python3.12-alpine AS templates
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ENV TEMPLATEFLOW_HOME="/templateflow"
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RUN uv pip install --system templateflow
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COPY docker/fetch_templates.py fetch_templates.py
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RUN python fetch_templates.py
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# FreeSurfer 7.3.2
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FROM downloader as freesurfer
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COPY docker/files/freesurfer7.3.2-exclude.txt /usr/local/etc/freesurfer7.3.2-exclude.txt
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RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer-linux-ubuntu22_amd64-7.3.2.tar.gz \
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| tar zxv --no-same-owner -C /opt --exclude-from=/usr/local/etc/freesurfer7.3.2-exclude.txt
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# AFNI
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FROM downloader as afni
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# Bump the date to current to update AFNI
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RUN echo "2024.03.08"
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RUN mkdir -p /opt/afni-latest \
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&& curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
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| tar -xz -C /opt/afni-latest --strip-components 1 \
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--exclude "linux_openmp_64/*.gz" \
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--exclude "linux_openmp_64/funstuff" \
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--exclude "linux_openmp_64/shiny" \
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--exclude "linux_openmp_64/afnipy" \
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--exclude "linux_openmp_64/lib/RetroTS" \
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--exclude "linux_openmp_64/lib_RetroTS" \
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--exclude "linux_openmp_64/meica.libs" \
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# Keep only what we use
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&& find /opt/afni-latest -type f -not \( \
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-name "3dTshift" -or \
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-name "3dUnifize" -or \
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-name "3dAutomask" -or \
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-name "3dvolreg" \) -delete
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# Micromamba
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FROM downloader as micromamba
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# Install a C compiler to build extensions when needed.
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# traits<6.4 wheels are not available for Python 3.11+, but build easily.
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RUN apt-get update && \
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apt-get install -y --no-install-recommends build-essential && \
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apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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WORKDIR /
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# Bump the date to current to force update micromamba
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RUN echo "2024.03.08"
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RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
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ENV MAMBA_ROOT_PREFIX="/opt/conda"
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COPY env.yml /tmp/env.yml
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COPY requirements.txt /tmp/requirements.txt
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WORKDIR /tmp
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RUN micromamba create -y -f /tmp/env.yml && \
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micromamba clean -y -a
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#
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# Main stage
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#
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FROM ${BASE_IMAGE} AS base
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FROM ${BASE_IMAGE} as main
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# Configure apt
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ENV DEBIAN_FRONTEND="noninteractive" \
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LANG="en_US.UTF-8" \
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LC_ALL="en_US.UTF-8"
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# Some baseline tools; bc is needed for FreeSurfer, so don't drop it
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RUN apt-get update && \
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apt-get install -y --no-install-recommends \
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bc \
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ca-certificates \
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curl \
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git \
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gnupg \
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lsb-release \
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netbase \
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xvfb && \
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apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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# Configure PPAs for libpng12 and libxp6
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RUN GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/linuxuprising.gpg --recv 0xEA8CACC073C3DB2A \
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&& GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/zeehio.gpg --recv 0xA1301338A3A48C4A \
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&& echo "deb [signed-by=/usr/share/keyrings/linuxuprising.gpg] https://ppa.launchpadcontent.net/linuxuprising/libpng12/ubuntu jammy main" > /etc/apt/sources.list.d/linuxuprising.list \
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&& echo "deb [signed-by=/usr/share/keyrings/zeehio.gpg] https://ppa.launchpadcontent.net/zeehio/libxp/ubuntu jammy main" > /etc/apt/sources.list.d/zeehio.list
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# Dependencies for AFNI; requires a discontinued multiarch-support package from bionic (18.04)
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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ed \
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gsl-bin \
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libglib2.0-0 \
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libglu1-mesa-dev \
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libglw1-mesa \
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libgomp1 \
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libjpeg62 \
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libpng12-0 \
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libxm4 \
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libxp6 \
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netpbm \
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tcsh \
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xfonts-base \
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xvfb \
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&& curl -sSL --retry 5 -o /tmp/multiarch.deb http://archive.ubuntu.com/ubuntu/pool/main/g/glibc/multiarch-support_2.27-3ubuntu1.5_amd64.deb \
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&& dpkg -i /tmp/multiarch.deb \
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&& rm /tmp/multiarch.deb \
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&& apt-get install -f \
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&& apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
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&& gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" \
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&& if [ -n "$gsl2_path" ]; then \
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ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; \
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fi \
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&& ldconfig
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# Install files from stages
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COPY --from=freesurfer /opt/freesurfer /opt/freesurfer
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COPY --from=afni /opt/afni-latest /opt/afni-latest
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# Simulate SetUpFreeSurfer.sh
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ENV OS="Linux" \
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FS_OVERRIDE=0 \
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FIX_VERTEX_AREA="" \
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FSF_OUTPUT_FORMAT="nii.gz" \
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FREESURFER_HOME="/opt/freesurfer"
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ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
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FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \
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MNI_DIR="$FREESURFER_HOME/mni" \
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LOCAL_DIR="$FREESURFER_HOME/local" \
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MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
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MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
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MNI_DATAPATH="$FREESURFER_HOME/mni/data"
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ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
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MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
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PATH="$FREESURFER_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
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# AFNI config
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ENV PATH="/opt/afni-latest:$PATH" \
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AFNI_IMSAVE_WARNINGS="NO" \
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AFNI_PLUGINPATH="/opt/afni-latest"
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# Create a shared $HOME directory
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RUN useradd -m -s /bin/bash -G users niworkflows
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WORKDIR /home/niworkflows
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ENV HOME="/home/niworkflows"
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COPY --link --from=templates /templateflow /home/fmriprep/.cache/templateflow
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RUN chmod -R go=u $HOME
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ENV HOME="/home/niworkflows" \
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LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH"
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COPY --from=micromamba /bin/micromamba /bin/micromamba
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COPY --from=micromamba /opt/conda/envs/niworkflows /opt/conda/envs/niworkflows
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ENV MAMBA_ROOT_PREFIX="/opt/conda"
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RUN micromamba shell init -s bash && \
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echo "micromamba activate niworkflows" >> $HOME/.bashrc
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ENV PATH="/opt/conda/envs/niworkflows/bin:$PATH" \
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CPATH="/opt/conda/envs/niworkflows/include:$CPATH" \
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LD_LIBRARY_PATH="/opt/conda/envs/niworkflows/lib:$LD_LIBRARY_PATH"
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COPY docker/fetch_templates.py /tmp/fetch_templates.py
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RUN python /tmp/fetch_templates.py && \
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rm /tmp/fetch_templates.py && \
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find $HOME/.cache/templateflow -type d -exec chmod go=u {} + && \
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find $HOME/.cache/templateflow -type f -exec chmod go=u {} +
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# FSL environment
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ENV LANG="C.UTF-8" \
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LC_ALL="C.UTF-8" \
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PYTHONNOUSERSITE=1 \
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FSLDIR="/opt/conda/envs/fmriprep" \
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FSLOUTPUTTYPE="NIFTI_GZ" \
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FSLMULTIFILEQUIT="TRUE" \
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FSLLOCKDIR="" \
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FSLMACHINELIST="" \
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FSLREMOTECALL="" \
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FSLGECUDAQ="cuda.q"
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# Unless otherwise specified each process should only use one thread - nipype
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# will handle parallelization
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ENV MKL_NUM_THREADS=1 \
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OMP_NUM_THREADS=1
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COPY docker/files/nipype.cfg /home/niworkflows/.nipype/nipype.cfg
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WORKDIR /tmp
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# Installing niworkflows
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COPY --from=src /src/dist/*.whl .
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RUN pip install --no-cache-dir $( ls *.whl )[all]
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FROM base AS test
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COPY docker/files/nipype.cfg /home/niworkflows/.nipype/nipype.cfg
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COPY --link --from=build /app/.pixi/envs/test /app/.pixi/envs/test
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COPY --link --from=build /test-shell-hook.sh /shell-hook.sh
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RUN cat /shell-hook.sh >> $HOME/.bashrc
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ENV PATH="/app/.pixi/envs/test/bin:$PATH"
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# Cleanup and ensure perms.
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RUN rm -rf $HOME/.npm $HOME/.conda $HOME/.empty && \
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find $HOME -type d -exec chmod go=u {} + && \
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find $HOME -type f -exec chmod go=u {} +
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ENV FSLDIR="/app/.pixi/envs/test"
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# Final settings
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WORKDIR /tmp
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ARG BUILD_DATE
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ARG VCS_REF
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LABEL org.label-schema.build-date=$BUILD_DATE \
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org.label-schema.name="niworkflows" \
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org.label-schema.description="niworkflows - NeuroImaging workflows" \
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org.label-schema.url="https://github.com/nipreps/niworkflows" \
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org.label-schema.vcs-ref=$VCS_REF \
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org.label-schema.vcs-url="https://github.com/nipreps/niworkflows" \
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org.label-schema.version=$VERSION \
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org.label-schema.schema-version="1.0"

‎env.yml‎

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name: niworkflows
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channels:
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- https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
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- conda-forge
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# Update this ~yearly; last updated Mar 2025
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dependencies:
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- python=3.12
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# Intel Math Kernel Library for numpy
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- mkl=2024.2.2
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- mkl-service=2.4.2
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# Base scientific python stack; required by FSL, so pinned here
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- numpy=1.26
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- scipy=1.15
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- matplotlib=3.9
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- pandas=2.2
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- h5py=3.13
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# Dependencies compiled against numpy, best to stick with conda
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- scikit-image=0.25
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- scikit-learn=1.6
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# Utilities
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- graphviz=11.0
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# Workflow dependencies: ANTs
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- ants=2.5
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# 5.4.1 and 5.4.2 cause segfaults with ants
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# Try to remove this ASAP
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# https://github.com/conda-forge/ants-feedstock/issues/19
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- libitk=5.4.0
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# Workflow dependencies: FSL (versions pinned in 6.0.7.13)
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- fsl-bet2=2111.8
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- fsl-flirt=2111.2
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- fsl-fast4=2111.3
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- fsl-mcflirt=2111.0
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- fsl-miscmaths=2203.2
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- pip
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- pip:
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- -r requirements.txt

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