Dockerfile.base

# fMRIPrep Docker Container Image distribution
#
# 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"

# Bump the date to current to refresh curl/certificates/etc
RUN echo "2025.08.20"
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 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

# 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

#
# 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 downloaded files from stages
COPY --link --from=freesurfer /opt/freesurfer /opt/freesurfer
COPY --link --from=msm /usr/local/bin/msm /usr/local/bin/msm

# 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 \
                    libopenblas0-openmp \
                    lsb-release \
                    netbase \
                    perl \
                    tcsh \
                    xvfb && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*


# Install AFNI from Docker container
# Find libraries with `ldd $BINARIES | grep afni`
COPY --link --from=afni/afni_make_build:AFNI_25.2.09 \
    /opt/afni/install/libf2c.so  \
    /opt/afni/install/libmri.so  \
    /usr/local/lib/
COPY --link --from=afni/afni_make_build:AFNI_25.2.09 \
    /opt/afni/install/3dAutomask \
    /opt/afni/install/3dTshift \
    /opt/afni/install/3dUnifize \
    /opt/afni/install/3dvolreg \
    /usr/local/bin/

# Changing library paths requires a re-ldconfig
RUN ldconfig

# Simulate SetUpFreeSurfer.sh
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 config
ENV AFNI_IMSAVE_WARNINGS="NO"

# FSL environment
ENV LANG="C.UTF-8" \
    LC_ALL="C.UTF-8" \
    PYTHONNOUSERSITE=1 \
    FSLOUTPUTTYPE="NIFTI_GZ" \
    FSLMULTIFILEQUIT="TRUE" \
    FSLLOCKDIR="" \
    FSLMACHINELIST="" \
    FSLREMOTECALL="" \
    FSLGECUDAQ="cuda.q"