Dockerfile

# Generated by: Neurodocker version 0.7.0+0.gdc97516.dirty
# Latest release: Neurodocker version 0.9.5
# Timestamp: 2023/05/18 01:58:52 UTC
#
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
# pull request on our GitHub repository:
#
#     https://github.com/ReproNim/neurodocker

FROM ubuntu:bionic-20201119

USER root

ARG DEBIAN_FRONTEND="noninteractive"

ENV LANG="en_US.UTF-8" \
    LC_ALL="en_US.UTF-8" \
    ND_ENTRYPOINT="/neurodocker/startup.sh"
RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
    && apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           apt-utils \
           bzip2 \
           ca-certificates \
           curl \
           locales \
           unzip \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
    && dpkg-reconfigure --frontend=noninteractive locales \
    && update-locale LANG="en_US.UTF-8" \
    && chmod 777 /opt && chmod a+s /opt \
    && mkdir -p /neurodocker \
    && if [ ! -f "$ND_ENTRYPOINT" ]; then \
         echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
    &&   echo 'set -e' >> "$ND_ENTRYPOINT" \
    &&   echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" \
    &&   echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
    fi \
    && chmod -R 777 /neurodocker && chmod a+s /neurodocker

ENTRYPOINT ["/neurodocker/startup.sh"]

RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           gcc g++ lsb-core bsdtar jq libopenblas-dev tree openjdk-8-jdk libstdc++6 \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

ENV PATH="/opt/dcm2niix-v1.0.20190902/bin:$PATH"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           cmake \
           g++ \
           gcc \
           git \
           make \
           pigz \
           zlib1g-dev \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
    && cd /tmp/dcm2niix \
    && git fetch --tags \
    && git checkout v1.0.20190902 \
    && mkdir /tmp/dcm2niix/build \
    && cd /tmp/dcm2niix/build \
    && cmake  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20190902 .. \
    && make \
    && make install \
    && rm -rf /tmp/dcm2niix

ENV FSLDIR="/opt/fsl-6.0.2" \
    PATH="/opt/fsl-6.0.2/bin:$PATH" \
    FSLOUTPUTTYPE="NIFTI_GZ" \
    FSLMULTIFILEQUIT="TRUE" \
    FSLTCLSH="/opt/fsl-6.0.2/bin/fsltclsh" \
    FSLWISH="/opt/fsl-6.0.2/bin/fslwish" \
    FSLLOCKDIR="" \
    FSLMACHINELIST="" \
    FSLREMOTECALL="" \
    FSLGECUDAQ="cuda.q"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           bc \
           dc \
           file \
           libfontconfig1 \
           libfreetype6 \
           libgl1-mesa-dev \
           libgl1-mesa-dri \
           libglu1-mesa-dev \
           libgomp1 \
           libice6 \
           libxcursor1 \
           libxft2 \
           libxinerama1 \
           libxrandr2 \
           libxrender1 \
           libxt6 \
           sudo \
           wget \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading FSL ..." \
    && mkdir -p /opt/fsl-6.0.2 \
    && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.2-centos6_64.tar.gz \
    | tar -xz -C /opt/fsl-6.0.2 --strip-components 1 \
    && sed -i '$iecho Some packages in this Docker container are non-free' $ND_ENTRYPOINT \
    && sed -i '$iecho If you are considering commercial use of this container, please consult the relevant license:' $ND_ENTRYPOINT \
    && sed -i '$iecho https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence' $ND_ENTRYPOINT \
    && sed -i '$isource $FSLDIR/etc/fslconf/fsl.sh' $ND_ENTRYPOINT

RUN bash -c 'bash /opt/fsl-6.0.2/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.2'

ENV FREESURFER_HOME="/opt/freesurfer-7.3.2" \
    PATH="/opt/freesurfer-7.3.2/bin:$PATH"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           bc \
           libgomp1 \
           libxmu6 \
           libxt6 \
           perl \
           tcsh \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading FreeSurfer ..." \
    && mkdir -p /opt/freesurfer-7.3.2 \
    && curl -fsSL --retry 5 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer-linux-ubuntu18_amd64-7.3.2.tar.gz \
    | tar -xz -C /opt/freesurfer-7.3.2 --strip-components 1 \
         --exclude='freesurfer/average/mult-comp-cor' \
         --exclude='freesurfer/lib/cuda' \
         --exclude='freesurfer/lib/qt' \
         --exclude='freesurfer/subjects/V1_average' \
         --exclude='freesurfer/subjects/bert' \
         --exclude='freesurfer/subjects/cvs_avg35' \
         --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
         --exclude='freesurfer/subjects/fsaverage3' \
         --exclude='freesurfer/subjects/fsaverage4' \
         --exclude='freesurfer/subjects/fsaverage5' \
         --exclude='freesurfer/subjects/fsaverage6' \
         --exclude='freesurfer/subjects/fsaverage_sym' \
         --exclude='freesurfer/trctrain' \
    && sed -i '$isource "/opt/freesurfer-7.3.2/SetUpFreeSurfer.sh"' "$ND_ENTRYPOINT"

ENV LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2017b/v93/runtime/glnxa64:/opt/matlabmcr-2017b/v93/bin/glnxa64:/opt/matlabmcr-2017b/v93/sys/os/glnxa64:/opt/matlabmcr-2017b/v93/extern/bin/glnxa64" \
    MATLABCMD="/opt/matlabmcr-2017b/v93/toolbox/matlab"
RUN export TMPDIR="$(mktemp -d)" \
    && apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           bc \
           libncurses5 \
           libxext6 \
           libxmu6 \
           libxpm-dev \
           libxt6 \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading MATLAB Compiler Runtime ..." \
    && curl -fsSL --retry 5 -o "$TMPDIR/mcr.zip" https://ssd.mathworks.com/supportfiles/downloads/R2017b/deployment_files/R2017b/installers/glnxa64/MCR_R2017b_glnxa64_installer.zip \
    && unzip -q "$TMPDIR/mcr.zip" -d "$TMPDIR/mcrtmp" \
    && "$TMPDIR/mcrtmp/install" -destinationFolder /opt/matlabmcr-2017b -mode silent -agreeToLicense yes \
    && rm -rf "$TMPDIR" \
    && unset TMPDIR

ENV PATH="/opt/afni-latest:$PATH" \
    AFNI_PLUGINPATH="/opt/afni-latest"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           ed \
           gsl-bin \
           libglib2.0-0 \
           libglu1-mesa-dev \
           libglw1-mesa \
           libgomp1 \
           libjpeg62 \
           libxm4 \
           netpbm \
           tcsh \
           xfonts-base \
           xvfb \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && curl -sSL --retry 5 -o /tmp/toinstall.deb http://launchpadlibrarian.net/160108232/libxp6_1.0.2-1ubuntu1_amd64.deb \
    && dpkg -i /tmp/toinstall.deb \
    && rm /tmp/toinstall.deb \
    && curl -sSL --retry 5 -o /tmp/toinstall.deb http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb \
    && dpkg -i /tmp/toinstall.deb \
    && rm /tmp/toinstall.deb \
    && apt-get install -f \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" \
    && if [ -n "$gsl2_path" ]; then \
         ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; \
    fi \
    && ldconfig \
    && echo "Downloading AFNI ..." \
    && 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

ENV ANTSPATH="/opt/ants-2.3.4/" \
    PATH="/opt/ants-2.3.4:$PATH"
RUN  echo "Downloading ANTs ..." \
    && mkdir -p /opt/ants-2.3.4 \
    && curl -fsSL https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz \
    | tar -xz -C /opt/ants-2.3.4 --strip-components 1

RUN bash -c 'apt-get update && apt-get install -y gnupg2 && wget -O- http://neuro.debian.net/lists/xenial.de-fzj.full | tee /etc/apt/sources.list.d/neurodebian.sources.list && apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9 && apt-get update && apt-get install -y connectome-workbench=1.3.2-2~nd16.04+1'

RUN bash -c 'cd /opt/ && wget http://www.fmrib.ox.ac.uk/~steve/ftp/fix1.068.tar.gz && tar xvfz fix1.068.tar.gz && rm fix1.068.tar.gz'

RUN test "$(getent passwd mica)" || useradd --no-user-group --create-home --shell /bin/bash mica
USER mica

ENV CONDA_DIR="/opt/miniconda-22.11.1" \
    PATH="/opt/miniconda-22.11.1/bin:$PATH"
RUN export PATH="/opt/miniconda-22.11.1/bin:$PATH" \
    && echo "Downloading Miniconda installer ..." \
    && conda_installer="/tmp/miniconda.sh" \
    && curl -fsSL --retry 5 -o "$conda_installer" https://repo.anaconda.com/miniconda/Miniconda3-py39_22.11.1-1-Linux-x86_64.sh \
    && bash "$conda_installer" -b -p /opt/miniconda-22.11.1 \
    && rm -f "$conda_installer" \
    && conda config --system --prepend channels conda-forge \
    && conda config --system --set auto_update_conda false \
    && conda config --system --set show_channel_urls true \
    && sync && conda clean -y --all && sync \
    && conda create -y -q --name micapipe \
    && conda install -y -q --name micapipe \
           "python" \
           "aiohttp" \
           "aiosignal" \
           "asn1crypto" \
           "async-timeout" \
           "astropy" \
           "attrs" \
           "bokeh" \
           "cffi" \
           "charset-normalizer" \
           "click" \
           "contourpy" \
           "cryptography" \
           "cycler" \
           "fonttools" \
           "frozenlist" \
           "html5lib" \
           "idna" \
           "importlib-resources" \
           "jinja2" \
           "joblib" \
           "kiwisolver" \
           "lxml" \
           "markupsafe" \
           "matplotlib==3.4.3" \
           "multidict" \
           "nibabel==4.0.2" \
           "nilearn" \
           "numpy==1.21.5" \
           "packaging" \
           "pandas==1.4.4" \
           "pillow" \
           "pycparser" \
           "pyhanko-certvalidator" \
           "pyparsing" \
           "pypdf" \
           "pypng" \
           "python-bidi" \
           "python-dateutil" \
           "pytz" \
           "pytz-deprecation-shim" \
           "pyyaml" \
           "qrcode" \
           "reportlab" \
           "requests" \
           "scikit-learn" \
           "scikit-fmm" \
           "scipy" \
           "six" \
           "svglib" \
           "threadpoolctl" \
           "tinycss2" \
           "tornado" \
           "typing-extensions" \
           "tzlocal" \
           "uritools" \
           "urllib3" \
           "vtk==9.2.2" \
           "webencodings" \
           "wslink" \
           "yarl" \
           "zipp" \
           "pyvirtualdisplay==3.0" \
    && sync && conda clean -y --all && sync \
    && bash -c "source activate micapipe \
    &&   pip install --no-cache-dir  \
             "argparse==1.1" \
             "brainspace==0.1.10" \
             "tedana==0.0.12" \
             "duecredit" \
             "pyhanko==0.17.2" \
             "mapca==0.0.3" \
             "xhtml2pdf==0.2.9" \
             "oscrypto==1.3.0" \
             "tzdata==2022.7" \
             "arabic-reshaper==3.0.0" \
             "cssselect2==0.7.0" \
             "pygeodesic==0.1.8" \
             "seaborn==0.11.2"" \
    && rm -rf ~/.cache/pip/* \
    && sync \
    && sed -i '$isource activate micapipe' $ND_ENTRYPOINT

RUN bash -c 'source activate micapipe && conda install -c mrtrix3 mrtrix3==3.0.1 && pip install git+https://github.com/MICA-MNI/ENIGMA.git'

ENV PATH="/opt/FastSurfer:$PATH"
ENV FASTSURFER_HOME=/opt/FastSurfer
RUN git clone https://github.com/Deep-MI/FastSurfer.git /opt/FastSurfer && cd /opt/FastSurfer && git checkout stable && ls /opt/FastSurfer
RUN cd /opt/FastSurfer \
  && bash -c 'wget --no-check-certificate -qO /tmp/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-py38_4.11.0-Linux-x86_64.sh \
  && chmod +x /tmp/miniconda.sh \
  && /tmp/miniconda.sh -b -p /opt/conda \
  && rm /tmp/miniconda.sh \
  && conda env create -f ./fastsurfer_env_cpu.yml'

# Install FastSurferCNN module
ENV PYTHONPATH="${PYTHONPATH}:/opt/FastSurfer"
RUN bash -c "source activate fastsurfer_cpu && cd /opt/FastSurfer && python FastSurferCNN/download_checkpoints.py --all && source deactivate"

USER root

RUN apt-get update -qq && apt-get install -y -q --no-install-recommends xvfb && apt-get clean

# R and libraries
RUN set -uex; \
    LD_LIBRARY_PATH=/lib64/:${PATH}; \
    apt update; \
    apt install -y software-properties-common apt-transport-https; \
    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9; \
    add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'; \
    apt-get update; \
    apt-get install -y r-base libblas-dev liblapack-dev gfortran g++ libgl1-mesa-glx; \
    apt-get install -y r-base-dev; \
    rm -rf /var/lib/apt/lists/*;

COPY ./R_config/* /opt/

RUN bash -c 'bash /opt/install_R_env.sh && cd /opt/afni-latest && rPkgsInstall -pkgs ALL'

# Install c3d
RUN set -uex; \
    cd /opt/ && \
    wget -O itksnap.tar.gz https://sourceforge.net/projects/c3d/files/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz/download && \
    tar -xf itksnap.tar.gz -C /opt/ && \
    rm itksnap.tar.gz
ENV PATH="/opt/c3d-1.0.0-Linux-x86_64/bin:${PATH}"

COPY . /opt/micapipe/

RUN bash -c 'cd /opt/micapipe && mv fix_settings.sh /opt/fix1.068/settings.sh && mv fsl_conf/* /opt/fsl-6.0.2/etc/flirtsch/'

RUN bash -c 'cp -r /opt/micapipe/surfaces/fsaverage5 /opt/freesurfer-7.3.2/subjects'

WORKDIR /home/mica

ENV MICAPIPE="/opt/micapipe"

ENV PROC="container_micapipe-v0.2.3"

ENV FIXPATH=/opt/fix1.068

ENV PATH="/opt/fix1.068/:${PATH}"

ENV PATH="/opt/micapipe/:/opt/micapipe/functions:${PATH}"

ENTRYPOINT ["/neurodocker/startup.sh", "/opt/micapipe/micapipe"]