anchor.diff:      \n      "neurodebian:stretch-non-free" \
       \n    ], \
       \n    [ \
  -    \n      "instruction", \
  -    \n      "RUN curl -sL https://deb.nodesource.com/setup_6.x | bash -" \
  +    \n      "afni", \
  +    \n      { \
  +    \n        "version": "latest", \
  +    \n        "install_python2": "true" \
  +    \n      } \
  +    \n    ], \
  +    \n    [ \
  +    \n      "freesurfer", \
  +    \n      { \
  +    \n        "version": "6.0.0", \
  +    \n        "min": true \
  +    \n      } \
       \n    ], \
       \n    [ \
       \n      "install", \
       \n      [ \
  -    \n        "ants", \
       \n        "dcm2niix", \
       \n        "convert3d", \
  +    \n        "ants", \
  +    \n        "fsl", \
  +    \n        "gcc", \
  +    \n        "g++", \
       \n        "graphviz", \
       \n        "tree", \
       \n        "git-annex-standalone", \
  
positive.code:     && conda config --system --prepend channels conda-forge \
      && conda config --system --set auto_update_conda false \
      && conda config --system --set show_channel_urls true \
      && conda update -y -q --all && sync \
      && conda clean -tipsy && sync
  
  #-------------------------
  # Create conda environment
  #-------------------------
  RUN conda create -y -q --name neuro3 \
      	python=3.6 altair apptools bokeh codecov configobj cython joblib jupyter jupyter_contrib_nbextensions jupyterhub jupyterlab matplotlib nitime pandas reprounzip reprozip scikit-image scikit-learn seaborn swig traits traitsui \
      && sync && conda clean -tipsy && sync \
      && /bin/bash -c "source activate neuro3 \
      	&& pip install -q --no-cache-dir \
      	https://github.com/nipy/nipype/tarball/master https://github.com/nipy/nibabel/archive/master.zip https://github.com/INCF/pybids/archive/master.zip git+https://github.com/jupyterhub/nbserverproxy.git git+https://github.com/jupyterhub/nbrsessionproxy.git https://github.com/satra/mapalign/archive/master.zip datalad dipy duecredit nilearn nipy niworkflows pprocess pymvpa2" \
      && sync
  ENV PATH=/opt/conda/envs/neuro3/bin:$PATH
  
  # User-defined instruction
  RUN bash -c "source activate neuro3 && python -m ipykernel install --sys-prefix --name neuro3 --display-name Py3-neuro" 
  
  # User-defined instruction
  RUN bash -c "source activate neuro3 && pip install --no-cache-dir --pre --upgrade ipywidgets pythreejs" 
  
  # User-defined instruction
  RUN bash -c "source activate neuro3 && pip install --no-cache-dir --upgrade https://github.com/maartenbreddels/ipyvolume/archive/master.zip && jupyter nbextension install --py --sys-prefix ipyvolume && jupyter nbextension enable --py --sys-prefix ipyvolume" 
  
  # User-defined instruction
  RUN bash -c "source activate neuro3 && pip install --no-cache-dir git+https://github.com/data-8/gitautosync && jupyter serverextension enable --py nbgitautosync --sys-prefix" 
  
  # User-defined instruction
  RUN bash -c "source activate neuro3 && jupyter nbextension enable rubberband/main && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main && jupyter nbextension enable vega --py --sys-prefix" 
  
  # User-defined instruction
  RUN bash -c "source activate neuro3 && jupyter serverextension enable --sys-prefix --py nbserverproxy && jupyter serverextension enable --sys-prefix --py nbrsessionproxy && jupyter nbextension install --sys-prefix --py nbrsessionproxy && jupyter nbextension enable --sys-prefix --py nbrsessionproxy" 
  
  USER root
  
  # User-defined instruction
  RUN echo 'neuro:neuro' | chpasswd && usermod -aG sudo neuro
  
  # User-defined instruction
  RUN mkdir /data && chown neuro /data && chmod 777 /data && mkdir /output && chown neuro /output && chmod 777 /output && mkdir /repos && chown neuro /repos && chmod 777 /repos
  
  USER neuro
  
  # User-defined instruction
  RUN cd /repos && git clone https://github.com/neuro-data-science/neuroviz.git && git clone https://github.com/neuro-data-science/neuroML.git && git clone https://github.com/ReproNim/reproducible-imaging.git && git clone https://github.com/miykael/nipype_tutorial.git && git clone https://github.com/jmumford/nhwEfficiency.git && git clone https://github.com/jmumford/R-tutorial.git
  
  # User-defined instruction
  RUN bash -c "source activate neuro3 && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && datalad --on-failure ignore get -r -J4 ds000114/sub-01/ses-test/anat && datalad --on-failure ignore get -r -J4 ds000114/sub-01/ses-test/func/*fingerfootlips* && datalad --on-failure ignore get -r -J4 ds000114/derivatives/fmriprep/sub-01/anat && datalad --on-failure ignore get -r -J4 ds000114/derivatives/fmriprep/sub-01/ses-test/func/*fingerfootlips*" 
  
  # User-defined instruction
  RUN curl -sSL https://osf.io/dhzv7/download?version=3 | tar zx -C /data/ds000114/derivatives/fmriprep
  
  # User-defined instruction
  ENV LD_LIBRARY_PATH="/usr/lib/R/lib:${LD_LIBRARY_PATH}" 
  
  # User-defined instruction
  RUN bash -c "echo c.NotebookApp.ip = \'0.0.0.0\' > ~/.jupyter/jupyter_notebook_config.py" 
  
  WORKDIR /repos
  
  #--------------------------------------
  # Save container specifications to JSON
  
negative.code:     \n        "less", \
      \n        "ncdu", \
      \n        "tig", \
      \n        "git-annex-remote-rclone" \
      \n      ] \
      \n    ], \
      \n    [ \
      \n      "add_to_entrypoint", \
      \n      [ \
      \n        "source /etc/fsl/fsl.sh" \
      \n      ] \
      \n    ], \
      \n    [ \
      \n      "spm", \
  