Dockerfile

# This Dockerfile constructs a docker image, based on the vistalab/freesurfer-core
# docker image, that applies the retinotopic templates from Benson et al. (2014)
# PLOS Comput Biol to a FreeSurfer subject.
#
# Example build:
#   docker build --no-cache --tag scitran/retinotopy-templates `pwd`
#
# Example usage:
#   docker run -v /path/to/your/subject:/input scitran/retinotopy-templates
#

# Start with the Freesurfer container
FROM vistalab/freesurfer

# Note the Maintainer.
MAINTAINER Michael Perry <lmperry@stanford.edu>

# Install system dependencies
RUN apt-get -y update && apt-get -y install\
      g++ \
      make \
      python \
      python2.7 \
      python-dev \
      python-setuptools \
      python-igraph \
      python-numpy \
      python-scipy \
      libxml2 \
      libxml2-dev \
      zlib1g \
      zlib1g-dev \
      tar \
      zip \
      git \
      gawk \
      tcsh \
      perl-modules \
      libgomp1 \
      bc

# FREESURFER CONFIG
COPY license /opt/freesurfer/.license

# Download the occipital-atlas-contents
ENV OCADIR /opt/occipital-atlas/
WORKDIR ${OCADIR}
ADD https://storage.googleapis.com/flywheel/gears/data/occipital-atlas/occipital-atlas-contents.tar.gz /opt/occipital-atlas/
RUN tar -xf occipital-atlas-contents.tar.gz && \
      rm -f occipital-atlas-contents.tar.gz

# Move relevant files over from contents
RUN rsync -avP ${OCADIR}/contents/subjects/fsaverage_sym /opt/freesurfer/subjects/ && \
      rm -rf ${OCADIR}/contents/subjects/fsaverage_sym && \
      rsync -avP ${OCADIR}/contents/subjects/fsaverage /opt/freesurfer/subjects/ && \
      rm -rf ${OCADIR}/contents/subjects/fsaverage && \
      mv ${OCADIR}/contents/LICENSE.txt / && \
      mv ${OCADIR}/contents/README.md /

# Copy bin code to container
COPY bin/apply_template.sh /opt/share/retinotopy-template/apply_template.sh
COPY bin/run_apply_template.sh /opt/share/retinotopy-template/run_apply_template.sh

# Make sure the scripts are executable.
RUN chmod +x /opt/share/retinotopy-template/apply_template.sh
RUN chmod +x /opt/share/retinotopy-template/run_apply_template.sh

# Install python, and configure neuropythy library
WORKDIR /opt
RUN git clone https://github.com/noahbenson/neuropythy

WORKDIR /opt/neuropythy
RUN python setup.py install && \
      chmod +x /opt/neuropythy/surf2ribbon && \
      ln -s /opt/neuropythy/surf2ribbon /usr/bin/surf2ribbon && \
      ln -s /opt/neuropythy/surf2surf /usr/bin/surf2surf

# Make directory for flywheel spec (v0)
ENV FLYWHEEL /flywheel/v0
RUN mkdir -p ${FLYWHEEL}

# Copy and configure run script and metadata code
COPY bin/run \
      bin/parse_config.py \
      bin/srf2obj \
      manifest.json \
      ${FLYWHEEL}/

# Copy the default config.json file to the container
COPY bin/config.json ${FLYWHEEL}/default_config.json

# Handle file properties for execution
RUN chmod +x \
      ${FLYWHEEL}/run \
      ${FLYWHEEL}/parse_config.py \
      ${FLYWHEEL}/srf2obj

# We run the run_apply_template.sh script on entry.
ENTRYPOINT ["/flywheel/v0/run"]