chore(docker): Fetch mri_vol2vol from FreeSurfer image, pare down Dockerfile

Author: effigies

.circleci/config.yml

@@ -141,7 +141,7 @@ jobs:
               -w /src/nitransforms -v $PWD:/src/nitransforms \
               -v /tmp/data/nitransforms-tests:/data -e TEST_DATA_HOME=/data \
               -e COVERAGE_FILE=/tmp/coverage/.pytest.coverage \
-              -v /tmp/fslicense/license.txt:/opt/freesurfer/license.txt:ro \
+              -v /tmp/fslicense/license.txt:/usr/local/freesurfer/license.txt:ro \
               -v /tmp/tests:/tmp nitransforms:latest \
               pytest --junit-xml=/tmp/summaries/pytest.xml \
                      --cov nitransforms --cov-report xml:/tmp/coverage/unittests.xml \

Dockerfile

@@ -1,5 +1,5 @@
 # Ubuntu 22.04 LTS - Jammy
-ARG BASE_IMAGE=ubuntu:jammy-20240125
+ARG BASE_IMAGE=ubuntu:jammy-20250730
 
 #
 # Build wheel
@@ -14,9 +14,9 @@ RUN uv build --wheel /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 echo "2025.09.25"
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
                     binutils \
@@ -28,64 +28,47 @@ RUN apt-get update && \
 
 RUN update-ca-certificates -f
 
-# FreeSurfer 7.3.2
-FROM downloader as freesurfer
-COPY docker/files/freesurfer7.3.2-exclude.txt /usr/local/etc/freesurfer7.3.2-exclude.txt
-COPY docker/files/fs-cert.pem /usr/local/etc/fs-cert.pem
-RUN curl --cacert /usr/local/etc/fs-cert.pem \
-     -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
-
 # 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.
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends build-essential && \
-    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+FROM downloader AS micromamba
 
 WORKDIR /
 # Bump the date to current to force update micromamba
-RUN echo "2024.02.06"
+RUN echo "2025.09.05"
 RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
 
 ENV MAMBA_ROOT_PREFIX="/opt/conda"
 COPY env.yml /tmp/env.yml
-# COPY requirements.txt /tmp/requirements.txt
 WORKDIR /tmp
 RUN micromamba create -y -f /tmp/env.yml && \
     micromamba clean -y -a
 
 #
 # Main stage
 #
-FROM ${BASE_IMAGE} as nitransforms
+FROM ${BASE_IMAGE} AS nitransforms
 
 # Configure apt
 ENV DEBIAN_FRONTEND="noninteractive" \
     LANG="en_US.UTF-8" \
     LC_ALL="en_US.UTF-8"
 
-# Some baseline tools; bc is needed for FreeSurfer, so don't drop it
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
-                    bc \
-                    ca-certificates \
-                    curl \
-                    libgomp1 \
-                    lsb-release \
-                    netbase \
-                    xvfb && \
+        libexpat1 \
+        libgomp1 \
+        && \
     apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-# Install files from stages
-COPY --from=freesurfer /opt/freesurfer /opt/freesurfer
+# Install FreeSurfer and AFNI bins from images
+COPY --from=freesurfer/freesurfer:7.4.1 \
+    /usr/local/freesurfer/bin/mri_vol2vol \
+    /usr/local/freesurfer/bin/
 COPY --from=afni/afni_make_build:AFNI_25.2.09 \
     /opt/afni/install/libf2c.so \
     /opt/afni/install/libmri.so \
     /usr/local/lib/
 COPY --from=afni/afni_make_build:AFNI_25.2.09 \
+    /opt/afni/install/3dAllineate \
     /opt/afni/install/3dNwarpApply \
     /opt/afni/install/3dWarp \
     /opt/afni/install/3drefit \
@@ -97,41 +80,27 @@ ENV OS="Linux" \
     FS_OVERRIDE=0 \
     FIX_VERTEX_AREA="" \
     FSF_OUTPUT_FORMAT="nii.gz" \
-    FREESURFER_HOME="/opt/freesurfer"
+    FREESURFER_HOME="/usr/local/freesurfer"
 ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
     FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \
-    MNI_DIR="$FREESURFER_HOME/mni" \
     LOCAL_DIR="$FREESURFER_HOME/local" \
-    MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
-    MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
-    MNI_DATAPATH="$FREESURFER_HOME/mni/data"
-ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
-    MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
-    PATH="$FREESURFER_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
+    PATH="$FREESURFER_HOME/bin:$PATH"
 
 # AFNI config
-ENV PATH="/opt/afni-latest:$PATH" \
-    AFNI_IMSAVE_WARNINGS="NO" \
-    AFNI_PLUGINPATH="/opt/afni-latest"
-
-# Workbench config
-ENV PATH="/opt/workbench/bin_linux64:$PATH"
+ENV AFNI_IMSAVE_WARNINGS="NO"
 
 # Create a shared $HOME directory
 RUN useradd -m -s /bin/bash -G users neuro
 WORKDIR /home/neuro
-ENV HOME="/home/neuro" \
-    LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH"
+ENV HOME="/home/neuro"
 
 COPY --from=micromamba /bin/micromamba /bin/micromamba
 COPY --from=micromamba /opt/conda/envs/nitransforms /opt/conda/envs/nitransforms
 
 ENV MAMBA_ROOT_PREFIX="/opt/conda"
 RUN micromamba shell init -s bash && \
     echo "micromamba activate nitransforms" >> $HOME/.bashrc
-ENV PATH="/opt/conda/envs/nitransforms/bin:$PATH" \
-    CPATH="/opt/conda/envs/nitransforms/include:$CPATH" \
-    LD_LIBRARY_PATH="/opt/conda/envs/nitransforms/lib:$LD_LIBRARY_PATH"
+ENV PATH="/opt/conda/envs/nitransforms/bin:$PATH"
 
 # FSL environment
 ENV LANG="C.UTF-8" \
@@ -145,22 +114,10 @@ ENV LANG="C.UTF-8" \
     FSLREMOTECALL="" \
     FSLGECUDAQ="cuda.q"
 
-# Unless otherwise specified each process should only use one thread - nipype
-# will handle parallelization
-ENV MKL_NUM_THREADS=1 \
-    OMP_NUM_THREADS=1
-
 # Install package
-# CRITICAL: Make sure python setup.py --version has been run at least once
-#           outside the container, with access to the git history.
 COPY --from=src /src/dist/*.whl .
 RUN python -m pip install --no-cache-dir $( ls *.whl )[all]
 
-
-RUN find $HOME -type d -exec chmod go=u {} + && \
-    find $HOME -type f -exec chmod go=u {} + && \
-    rm -rf $HOME/.npm $HOME/.conda $HOME/.empty
-
 RUN ldconfig
 WORKDIR /tmp/