Dockerfile.base

# ASLPrep Docker Container Image distribution
#
# Base image: runtime environment without the aslprep package.
# Built separately and referenced by the main Dockerfile (like fMRIPrep).
#
# MIT License
#
# Copyright (c) The NiPreps Developers
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.

# Ubuntu 22.04 LTS - Jammy
ARG BASE_IMAGE=ubuntu:jammy-20250730

#
# Download stages
#

# Utilities for downloading packages
FROM ${BASE_IMAGE} AS downloader
ENV DEBIAN_FRONTEND="noninteractive" \
    LANG="en_US.UTF-8" \
    LC_ALL="en_US.UTF-8" \
    HOME="/home/aslprep"

# Bump the date to refresh curl/certificates/etc
RUN echo "2025.02.12"
RUN apt-get update && \
    apt-get install -y --no-install-recommends \
                    binutils \
                    bzip2 \
                    ca-certificates \
                    curl \
                    unzip && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# FreeSurfer 7.3.2 from official Ubuntu 22 tarball (same glibc as base; avoids Docker-image mismatch)
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

# FreeSurfer 7.4.1: only mri_synthseg / mri_synthstrip and models (Python scripts)
FROM freesurfer/freesurfer:7.4.1 AS freesurfer741

# MSM HOCR (Nov 19, 2019 release)
FROM downloader AS msm
RUN curl -L -H "Accept: application/octet-stream" https://api.github.com/repos/ecr05/MSM_HOCR/releases/assets/16253707 -o /usr/local/bin/msm \
    && chmod +x /usr/local/bin/msm

# AFNI
FROM downloader AS afni
RUN mkdir -p /opt/afni-latest \
    && curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
    | tar -xz -C /opt/afni-latest --strip-components 1 \
    --exclude "linux_openmp_64/*.gz" \
    --exclude "linux_openmp_64/funstuff" \
    --exclude "linux_openmp_64/shiny" \
    --exclude "linux_openmp_64/afnipy" \
    --exclude "linux_openmp_64/lib/RetroTS" \
    --exclude "linux_openmp_64/lib_RetroTS" \
    --exclude "linux_openmp_64/meica.libs" \
    && find /opt/afni-latest -type f -not \( \
        -name "3dTshift" -or \
        -name "3dUnifize" -or \
        -name "3dAutomask" -or \
        -name "3dAutobox" -or \
        -name "3dresample" -or \
        -name "3dZeropad" -or \
        -name "3dvolreg" \) -delete

#
# Main stage
#
FROM ${BASE_IMAGE} AS base

# Configure apt
ENV DEBIAN_FRONTEND="noninteractive" \
    LANG="en_US.UTF-8" \
    LC_ALL="en_US.UTF-8"

# Install from download stages
COPY --link --from=freesurfer /opt/freesurfer /opt/freesurfer
COPY --link --from=freesurfer741 /usr/local/freesurfer/python/scripts/mri_synthseg /opt/freesurfer/bin/mri_synthseg
COPY --link --from=freesurfer741 /usr/local/freesurfer/python/scripts/mri_synthstrip /opt/freesurfer/bin/mri_synthstrip
COPY --link --from=freesurfer741 /usr/local/freesurfer/models /opt/freesurfer/models
COPY --link --from=msm /usr/local/bin/msm /usr/local/bin/msm
COPY --link --from=afni /opt/afni-latest /opt/afni-latest

RUN chmod +x /opt/freesurfer/bin/mri_synthseg /opt/freesurfer/bin/mri_synthstrip

# Baseline system packages (bc for FreeSurfer; libs for Workbench/FSL)
RUN apt-get update && \
    apt-get install -y --no-install-recommends \
                    bc \
                    ca-certificates \
                    curl \
                    git \
                    gnupg \
                    libgomp1 \
                    libopenblas0-openmp \
                    lsb-release \
                    netbase \
                    xvfb && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# PPAs and packages for FreeSurfer/Workbench (libpng12, libxp, netpbm, etc.)
RUN GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/linuxuprising.gpg --recv 0xEA8CACC073C3DB2A \
    && GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/zeehio.gpg --recv 0xA1301338A3A48C4A \
    && 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 \
    && 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

RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           ed \
           gsl-bin \
           libglib2.0-0 \
           libglu1-mesa-dev \
           libglw1-mesa \
           libjpeg62 \
           libpng12-0 \
           libxm4 \
           libxp6 \
           netpbm \
           tcsh \
           xfonts-base \
    && 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 \
    && dpkg -i /tmp/multiarch.deb \
    && rm /tmp/multiarch.deb \
    && apt-get install -f \
    && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
    && gsl2_path="$(find / -name 'libgsl.so.19' 2>/dev/null || printf '')" \
    && if [ -n "$gsl2_path" ]; then ln -sfv "$gsl2_path" "$(dirname "$gsl2_path")/libgsl.so.0"; fi \
    && ldconfig

# Download atlases from AtlasPack (stored in tar.gz file on Box)
RUN mkdir -p "/home/aslprep/.cache/aslprep" && \
    curl -o AtlasPack.tar.gz -sSL "https://upenn.box.com/shared/static/0gxdoe77tuih5p9ainn4utdqj3kcq7p1.tar.gz" && \
    tar -xzf AtlasPack.tar.gz && \
    mv AtlasPack "/home/aslprep/.cache/aslprep/AtlasPack" && \
    rm AtlasPack.tar.gz

# Download XCP-D atlases (stored in tar.gz file on Box)
RUN mkdir -p "/home/aslprep/.cache/aslprep" && \
    curl -o XCPDAtlases.tar.gz -sSL "https://upenn.box.com/shared/static/4amxp72grenmp1up689k5oyn1i6nhunq.tar.gz" && \
    tar -xzf XCPDAtlases.tar.gz && \
    mv XCPDAtlases "/home/aslprep/.cache/aslprep/XCPDAtlases" && \
    rm XCPDAtlases.tar.gz && \
    find "/home/aslprep/.cache/aslprep" -type d -exec chmod go=u {} + && \
    find "/home/aslprep/.cache/aslprep" -type f -exec chmod go=u {} +

# FreeSurfer environment
ENV OS="Linux" \
    FS_OVERRIDE=0 \
    FIX_VERTEX_AREA="" \
    FSF_OUTPUT_FORMAT="nii.gz" \
    FREESURFER_HOME="/opt/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"

# AFNI
ENV PATH="/opt/afni-latest:$PATH" \
    AFNI_IMSAVE_WARNINGS="NO" \
    AFNI_PLUGINPATH="/opt/afni-latest"

# FSL / runtime (FSLDIR is set in the main Dockerfile, pointing to the pixi env)
ENV LANG="C.UTF-8" \
    LC_ALL="C.UTF-8" \
    PYTHONNOUSERSITE=1 \
    FSLOUTPUTTYPE="NIFTI_GZ" \
    FSLMULTIFILEQUIT="TRUE" \
    FSLLOCKDIR="" \
    FSLMACHINELIST="" \
    FSLREMOTECALL="" \
    FSLGECUDAQ="cuda.q"

RUN ldconfig
WORKDIR /tmp

LABEL org.label-schema.name="aslprep-base" \
      org.label-schema.description="ASLPrep base image - runtime dependencies without the aslprep package" \
      org.label-schema.url="https://aslprep.readthedocs.io/" \
      org.label-schema.vcs-url="https://github.com/PennLINC/aslprep" \
      org.label-schema.schema-version="1.0"