anchor.diff:  # Acquire script to be executed
   RUN cd ../ && wget https://raw.githubusercontent.com/BIDS-Apps/MRtrix3_connectome/master/run.py && chmod 775 run.py
   
  -# Setup environment variables 
  +# Setup environment variables
   ENV FREESURFER_HOME=/opt/freesurfer
   ENV FSLDIR=/usr/share/fsl/5.0
   ENV FSLOUTPUTTYPE=NIFTI_GZ
  
positive.code: ENV PATH=/opt/freesurfer/bin:/usr/lib/fsl/5.0:/usr/lib/ants:/mrtrix3/release/bin:/mrtrix3/scripts:$PATH
  ENV PYTHONPATH=/mrtrix3/scripts
  
  # Copied from another dockerfile; not sure...
  RUN mkdir /oasis
  RUN mkdir /projects
  RUN mkdir /scratch
  RUN mkdir /local-scratch
  
  # Target mount points
  RUN mkdir /bids_dataset
  RUN mkdir /outputs
  
  ENTRYPOINT ["/run.py"]
  
negative.code: RUN apt-get install -y ants
  RUN apt-get install -y fsl-5.0-core
  RUN apt-get install -y fsl-5.0-eddy-nonfree
  RUN apt-get install -y fsl-first-data
  RUN wget -qO- ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-HCP/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP.tar.gz | tar zxv -C /opt
  # TODO Acquire own FreeSurfer license file
  RUN echo $'fsa@brain.org.au\n13477\n*CCll67nWRT9.\n' > /opt/freesurfer/license
  