ENH: initial commit

Author: miykael

Dockerfile

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+# This Dockerfile is based on the dockerfile 'fmriprep' from the Poldrack
+# Lab (https://github.com/poldracklab/fmriprep).
+#
+# This means that the same copyrights apply to this Dockerfile, as they do for
+# the above mentioned dockerfile. For more information see:
+# https://github.com/miykael/nipype_tutorial
+FROM andrewosh/binder-base
+
+MAINTAINER Michael Notter <[email protected]>
+
+# Switch to root user for installation
+USER root
+
+#---------------------------------------------
+# Update OS dependencies and setup neurodebian
+#---------------------------------------------
+USER root
+RUN ln -snf /bin/bash /bin/sh
+ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get update && \
+    apt-get install -yq --no-install-recommends bzip2 ca-certificates curl git tree unzip wget xvfb zip
+ENV NEURODEBIAN_URL http://neuro.debian.net/lists/jessie.de-md.full
+RUN curl -sSL $NEURODEBIAN_URL | tee /etc/apt/sources.list.d/neurodebian.sources.list && \
+    apt-key adv --recv-keys --keyserver hkp://pgp.mit.edu:80 0xA5D32F012649A5A9 && \
+    apt-get update -qq
+
+#---------------------
+# Install FSL and AFNI
+#---------------------
+USER root
+RUN apt-get update && \
+    apt-get install -y -qq --no-install-recommends fsl-core fsl-atlases afni
+ENV FSLDIR=/usr/share/fsl/5.0 \
+    FSLOUTPUTTYPE=NIFTI_GZ \
+    FSLMULTIFILEQUIT=TRUE \
+    POSSUMDIR=/usr/share/fsl/5.0 \
+    LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH \
+    FSLTCLSH=/usr/bin/tclsh \
+    FSLWISH=/usr/bin/wish \
+    AFNI_MODELPATH=/usr/lib/afni/models \
+    AFNI_IMSAVE_WARNINGS=NO \
+    AFNI_TTATLAS_DATASET=/usr/share/afni/atlases \
+    AFNI_PLUGINPATH=/usr/lib/afni/plugins \
+    PATH=/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH
+
+#-----------------------------------------------------
+# Update conda and pip dependencies (including Nipype)
+#-----------------------------------------------------
+RUN conda update conda --yes --quiet
+RUN conda config --add channels conda-forge
+RUN conda install --yes --quiet ipython \
+                                pip \
+                                jupyter \
+                                notebook \
+                                nb_conda \
+                                nb_conda_kernels \
+                                matplotlib \
+                                graphviz \
+                                pandas \
+                                seaborn \
+                                nipype
+RUN python -c "from matplotlib import font_manager"
+
+# Clean up Python3 environment and delete not needed packages
+RUN conda remove --name python3 --all --yes --quiet && \
+    conda remove qt pyqt scikit-image scikit-learn sympy --yes --quiet && \
+    conda clean -tipsy
+
+#---------------------------------------------
+# Install graphviz and update pip dependencies
+#---------------------------------------------
+USER root
+RUN apt-get install -yq --no-install-recommends graphviz
+USER $NB_USER
+RUN pip install --upgrade --quiet pip && \
+    pip install --upgrade --quiet nipy \
+                                  rdflib \
+                --ignore-installed && \
+    rm -rf ~/.cache/pip
+
+#-----------------------------------------------------
+# Clear apt cache and delete unnecessary folders
+#-----------------------------------------------------
+RUN apt-get clean remove -y && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /boot /media /mnt /opt /srv
+
+ENV SHELL /bin/bash

LICENSE

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+Copyright (c) 2017,
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of crn_base nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

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+# Nipype Tutorial Notebooks
+
+The Nipype tutorial runs on [mybinder.org](http://mybinder.org/) and can be started by clicking on the following button: [![Binder](http://mybinder.org/badge.svg)](http://mybinder.org/repo/miykael/nipype_tutorial)
+
+The Dockerfile that creates the nipype environment on mybinder is based on the docker image [miykael/nipype_basic](https://hub.docker.com/r/miykael/nipype_basic/).
+
+
+## The Dataset
+
+The data used for this tutorial is from [openfmri.org](https://openfmri.org/) and is structured according the new and fancy [Brain Imaging Data Structure (BIDS)](http://bids.neuroimaging.io/).
+
+The dataset ds102 used for this tutorial was shortened to only three subjects, *sub-01*, *sub-02* and *sub-03*. For more information about the dataset, see the [description on openfmri.org](https://openfmri.org/dataset/ds000102/).
+
+
+## Feedback, Help & Support
+
+If you want to help us with this tutorial or have any questions, fell free to fork our repo [github.com/miykael/nipype_tutorial](https://github.com/miykael/nipype_tutorial) or interact with other contributors on the slack channel [brainhack.slack.com/messages/nipype/](https://brainhack.slack.com/messages/nipype/)