anchor.diff:      apt-get update && \
       apt-get install -y git-lfs
   
  -#---------AFNI INSTALL--------------------------------------------------------#
  -# setup of AFNI, which provides robust modifications of many of neuroimaging
  -# algorithms
  -RUN apt-get update -qq && apt-get install -yq --no-install-recommends ed gsl-bin libglu1-mesa-dev libglib2.0-0 libglw1-mesa fsl-atlases \
  -    libgomp1 libjpeg62 libxm4 netpbm tcsh xfonts-base xvfb && \
  -    libs_path=/usr/lib/x86_64-linux-gnu && \
  -    if [ -f $libs_path/libgsl.so.19 ]; then \
  -           ln $libs_path/libgsl.so.19 $libs_path/libgsl.so.0; \
  -    fi
  -
  -RUN mkdir -p /opt/afni && \
  -    curl -o afni.tar.gz -sSLO "$AFNI_URL" && \
  -    tar zxv -C /opt/afni --strip-components=1 -f afni.tar.gz && \
  -    rm -rf afni.tar.gz
  -ENV PATH=/opt/afni:$PATH
  -
  -#--------ANTS SETUP-----------------------------------------------------------#
  -RUN wget -qO- "https://cmake.org/files/v3.12/cmake-3.12.1-Linux-x86_64.tar.gz" | \
  -  tar --strip-components=1 -xz -C /usr/local
  -
  -ENV ANTS_VERSION=2.2.0
  -WORKDIR /tmp
  -RUN git clone git://github.com/stnava/ANTs.git ants \
  -    && cd ants \
  -    && mkdir build \
  -    && cd build \
  -    && cmake .. \
  -    && make -j8 \
  -    && mkdir -p /opt/ants \
  -    && mv bin/* /opt/ants && mv ../Scripts/* /opt/ants \
  -    && cd .. \
  -    && rm -rf build
  -
  -ENV ANTSPATH=/opt/ants/ \
  -    PATH=/opt/ants:$PATH
   #--------NDMG SETUP-----------------------------------------------------------#
   # setup of python dependencies for ndmg itself, as well as file dependencies
   RUN \
  -    pip install setuptools numpy networkx nibabel dipy scipy python-dateutil pandas boto3 awscli matplotlib nilearn sklearn pandas cython vtk pyvtk fury awscli requests scikit-image ipython duecredit --upgrade
  +    pip3.6 install numpy
   
   RUN \
  -    pip install plotly==1.12.9 pybids==0.6.4
  +    pip3.6 install networkx nibabel dipy scipy python-dateutil pandas boto3 awscli matplotlib nilearn sklearn pandas cython vtk pyvtk fury awscli requests scikit-image ipython duecredit
  +
  +RUN \
  +    pip3.6 install plotly==1.12.9 pybids==0.6.4 setuptools>=40.0
   
   WORKDIR /
  -
  -# Delete buggy line in dipy
  -RUN sed -i -e '189d;190d' /usr/local/lib/python2.7/dist-packages/dipy/tracking/eudx.py
   
   RUN mkdir /data && \
       chmod -R 777 /data
  
positive.code: RUN chmod -R 777 /usr/local/bin/ndmg_bids
  
  # and add it as an entrypoint
  ENTRYPOINT ["ndmg_bids"]
  
negative.code: RUN mkdir /outputs && \
      chmod -R 777 /outputs
  
  RUN git clone -b remove-zindex $NDMG_URL /ndmg && \
      cd /ndmg && \
      python3.6 setup.py install
  
  RUN mkdir /ndmg_atlases
  
  