Merge pull request #48 from brainprepdesk/dev

containers/Dockerfile.quasiraw

@@ -1,16 +1,16 @@
-FROM ubuntu:22.04
+FROM ubuntu:22.04 AS ubuntu_base
 
 ENV DEBIAN_FRONTEND="noninteractive" \
     LANG="en_US.UTF-8" \
     LC_ALL="en_US.UTF-8"
 RUN apt-get update -qq \
     && apt-get install -y -q --no-install-recommends \
-           apt-utils \
-           bzip2 \
-           ca-certificates \
-           curl \
-           locales \
-           unzip \
+    apt-utils \
+    bzip2 \
+    ca-certificates \
+    curl \
+    locales \
+    unzip \
     && rm -rf /var/lib/apt/lists/*
 RUN sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
     && dpkg-reconfigure --frontend=noninteractive locales \
@@ -20,8 +20,6 @@ RUN sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
 # Parameters
 ENV ANTS_VERSION="2.6.2" \
     FSL_VERSION="6.0.7.19" \
-    FS_VERSION="8.1.0" \
-    FS_URL="https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/8.1.0/freesurfer_ubuntu22-8.1.0_amd64.deb" \
     ANTS_URL="https://github.com/ANTsX/ANTs/releases/download/v2.6.2/ants-2.6.2-centos7-X64-gcc.zip"
 
 # Install: FSL
@@ -37,145 +35,54 @@ ENV FSLDIR="/opt/fsl" \
     FSLGECUDAQ="cuda.q"
 RUN apt-get update -qq \
     && apt-get install -y -q --no-install-recommends \
-           bc \
-           ca-certificates \
-           curl \
-           dc \
-           file \
-           libfontconfig1 \
-           libfreetype6 \
-           libgl1-mesa-dev \
-           libgl1-mesa-dri \
-           libglu1-mesa-dev \
-           libgomp1 \
-           libice6 \
-           libopenblas0 \
-           libxcursor1 \
-           libxft2 \
-           libxinerama1 \
-           libxrandr2 \
-           libxrender1 \
-           libxt6 \
-           nano \
-           python3 \
-           sudo \
-           wget \
+    bc \
+    ca-certificates \
+    curl \
+    dc \
+    file \
+    libfontconfig1 \
+    libfreetype6 \
+    libgl1-mesa-dev \
+    libgl1-mesa-dri \
+    libglu1-mesa-dev \
+    libgomp1 \
+    libice6 \
+    libopenblas0 \
+    libxcursor1 \
+    libxft2 \
+    libxinerama1 \
+    libxrandr2 \
+    libxrender1 \
+    libxt6 \
+    nano \
+    python3 \
+    sudo \
+    wget \
     && rm -rf /var/lib/apt/lists/*
 RUN echo "Installing FSL ..." \
     && curl -fsSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | python3 - -d $FSLDIR -V $FSL_VERSION
 
-# Install: FreeSurfer
-ENV OS="Linux" \
-    PATH="/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:$PATH" \
-    FREESURFER_HOME="/opt/freesurfer" \
-    FREESURFER="/opt/freesurfer" \
-    SUBJECTS_DIR="/opt/freesurfer/subjects" \
-    LOCAL_DIR="/opt/freesurfer/local" \
-    FSFAST_HOME="/opt/freesurfer/fsfast" \
-    FMRI_ANALYSIS_DIR="/opt/freesurfer/fsfast" \
-    FUNCTIONALS_DIR="/opt/freesurfer/sessions" \
-    FS_OVERRIDE="0" \
-    FIX_VERTEX_AREA="" \
-    FSF_OUTPUT_FORMAT="nii.gz" \
-    MINC_BIN_DIR="/opt/freesurfer/mni/bin" \
-    MINC_LIB_DIR="/opt/freesurfer/mni/lib" \
-    MNI_DIR="/opt/freesurfer/mni" \
-    MNI_DATAPATH="/opt/freesurfer/mni/data" \
-    MNI_PERL5LIB="/opt/freesurfer/mni/share/perl5" \
-    PERL5LIB="/opt/freesurfer/mni/share/perl5"
-RUN apt-get update -qq \
-    && apt-get install -y -q --no-install-recommends \
-        octave \
-        wget \
-        language-pack-en \
-        binutils \
-        libx11-dev \
-        gettext \
-        xterm \
-        x11-apps \
-        perl \
-        make \
-        csh \
-        tcsh \
-        file \
-        bc \
-        xorg \
-        xorg-dev \
-        xserver-xorg-video-intel \
-        libncurses5 \
-        libbsd0 \
-        libegl1 \
-        libexpat1 \
-        libfontconfig1 \
-        libfreetype6 \
-        libgl1 \
-        libglib2.0-0 \
-        libglu1-mesa \
-        libglvnd0 \
-        libglx0 \
-        libgomp1 \
-        libice6 \
-        libicu70 \
-        libjpeg62 \
-        libmd0 \
-        libopengl0 \
-        libpcre2-16-0 \
-        libpng16-16 \
-        libquadmath0 \
-        libsm6 \
-        libx11-6 \
-        libx11-xcb1 \
-        libxau6 \
-        libxcb-icccm4 \
-        libxcb-image0 \
-        libxcb-keysyms1 \
-        libxcb-randr0 \
-        libxcb-render-util0 \
-        libxcb-render0 \
-        libxcb-shape0 \
-        libxcb-shm0 \
-        libxcb-sync1 \
-        libxcb-util1 \
-        libxcb-xfixes0 \
-        libxcb-xinerama0 \
-        libxcb-xinput0 \
-        libxcb-xkb1 \
-        libxcb1 \
-        libxdmcp6 \
-        libxext6 \
-        libxft2 \
-        libxi6 \
-        libxkbcommon-x11-0 \
-        libxkbcommon0 \
-        libxmu6 \
-        libxrender1 \
-        libxss1 \
-        libxt6 \
-        mesa-utils \
-        unzip \
-        libncurses5 \
-        libgomp1 \
-        openjdk-8-jdk \
-        xvfb \
-        xauth \
-    && rm -rf /var/lib/apt/lists/*
-RUN export TMPDIR="$(mktemp -d)"
-RUN echo "Downloading FreeSurfer ..." \
-    && curl -o $TMPDIR/freesurfer.deb $FS_URL
-RUN dpkg -i $TMPDIR/freesurfer.deb \
-    && rm -rf $TMPDIR \
-    && unset TMPDIR
-RUN ln -s /usr/local/freesurfer/${FS_VERSION} /opt/freesurfer
-RUN fs_install_mcr R2019b
+# -- SynthStrip build stage --
+FROM freesurfer/synthstrip:1.8 AS synthstrip
+# ----------------------------
+
+# Back in the main ubuntu build context
+FROM ubuntu_base AS main
+
+# Copy SynthStrip artifacts into main image
+ENV FREESURFER_HOME="/freesurfer"
+
+# Copy SynthStrip files from build stage
+COPY --from=synthstrip $FREESURFER_HOME $FREESURFER_HOME
 
 # Install ANTs
 ENV ANTSPATH="/opt/ants" \
     PATH="/opt/ants:$PATH"
 RUN apt-get update -qq \
     && apt-get install -y -q --no-install-recommends \
-           ca-certificates \
-           curl \
-           unzip \
+    ca-certificates \
+    curl \
+    unzip \
     && rm -rf /var/lib/apt/lists/*
 RUN echo "Downloading ANTs ..." \
     && curl -fsSL -o /opt/ants.zip $ANTS_URL
@@ -190,25 +97,33 @@ ENV PATH="/root/.pixi/bin:${PATH}"
 WORKDIR /opt/brainprep
 RUN apt-get update -qq \
     && apt-get install -y -q --no-install-recommends \
-           git \
+    git \
     && rm -rf /var/lib/apt/lists/*
 COPY pixi.toml .
 RUN pixi install
 RUN ln -s /opt/brainprep/.pixi/envs/default/bin/brainprep /usr/local/bin/brainprep
 
+# Wrapper in : /usr/local/bin
+# This script sets the PYTHONPATH locally only for mri_synthstrip
+RUN echo '#!/bin/bash\n\
+    PYTHONPATH="/freesurfer/env/lib/python3.10/site-packages" \
+    /usr/bin/python3 /freesurfer/mri_synthstrip "$@"' > /usr/local/bin/mri_synthstrip && \
+    chmod +x /usr/local/bin/mri_synthstrip
+ENV PATH="/usr/local/bin:$FREESURFER_HOME:$PATH
+
 COPY entrypoint.sh /opt/entrypoint.sh
 RUN chmod +x /opt/entrypoint.sh
 ENTRYPOINT ["/opt/entrypoint.sh"]
 ENV DEFAULT_ARGS="subject-level-quasiraw group-level-quasiraw"
 
 LABEL org.opencontainers.image.title="BrainPrep Quasi-Raw" \
-      org.opencontainers.image.description="Container for BrainPrep Quasi-Raw using FSL and FREESURFER" \
-      org.opencontainers.image.version="v2" \
-      org.opencontainers.image.licenses="CeCILL-B" \
-      org.opencontainers.image.authors="CEA/NeuroSpin/GAIA" \
-      org.opencontainers.image.documentation="https://brainprepdesk.github.io/brainprep/stable" \
-      org.opencontainers.image.source="https://github.com/brainprepdesk/brainprep" \
-      org.opencontainers.image.created="2025-01-15" \
-      com.brainprep.fsl.version="${FSL_VERSION}" \
-      com.brainprep.freesurfer.version="${FS_VERSION}" \
-      com.brainprep.ants.version="${ANTS_VERSION}"
+    org.opencontainers.image.description="Container for BrainPrep Quasi-Raw using FSL and FREESURFER" \
+    org.opencontainers.image.version="v2" \
+    org.opencontainers.image.licenses="CeCILL-B" \
+    org.opencontainers.image.authors="CEA/NeuroSpin/GAIA" \
+    org.opencontainers.image.documentation="https://brainprepdesk.github.io/brainprep/stable" \
+    org.opencontainers.image.source="https://github.com/brainprepdesk/brainprep" \
+    org.opencontainers.image.created="2025-01-15" \
+    com.brainprep.fsl.version="${FSL_VERSION}" \
+    com.brainprep.freesurfer.version="${FS_VERSION}" \
+    com.brainprep.ants.version="${ANTS_VERSION}"