ENH: add new neurodocker notebook

Author: miykael

notebooks/introduction_neurodocker.ipynb

@@ -0,0 +1,149 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Neurodocker tutorial\n",
+    "\n",
+    "[Neurodocker](https://github.com/kaczmarj/neurodocker) is a brilliant tool to create your own neuroimaging docker container. [Neurodocker](https://github.com/kaczmarj/neurodocker) is a command-line program that enables users to generate [Docker](http://www.docker.io/) containers that include neuroimaging software. These containers can be\n",
+    "converted to [Singularity](http://singularity.lbl.gov/) containers for use in high-performance computing\n",
+    "centers.\n",
+    "\n",
+    "Requirements:\n",
+    "\n",
+    "* [Docker](http://www.docker.io/)\n",
+    "* Internet connection"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Usage\n",
+    "\n",
+    "To view the Neurodocker help message\n",
+    "\n",
+    "    docker run --rm kaczmarj/neurodocker:v0.3.2 generate --help\n",
+    "\n",
+    "1. Users must specify a base Docker image and the package manager. Any Docker\n",
+    "   image on DockerHub can be used as your base image. Common base images\n",
+    "   include ``debian:stretch``, ``ubuntu:16.04``, ``centos:7``, and the various\n",
+    "   ``neurodebian`` images. If users would like to install software from the\n",
+    "   NeuroDebian repositories, it is recommended to use a ``neurodebian`` base\n",
+    "   image. The package manager is ``apt`` or ``yum``, depending on the base\n",
+    "   image.\n",
+    "2. Next, users should configure the container to fit their needs. This includes\n",
+    "   installing neuroimaging software, installing packages from the chosen package\n",
+    "   manager, installing Python and Python packages, copying files from the local\n",
+    "   machine into the container, and other operations. The list of supported\n",
+    "   neuroimaging software packages is available in the ``neurodocker`` help\n",
+    "   message.\n",
+    "3. The ``neurodocker`` command will generate a Dockerfile. This Dockerfile can\n",
+    "   be used to build a Docker image with the ``docker build`` command."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Create a Dockerfile with FSL, Python 3.6, and Nipype\n",
+    "\n",
+    "This command prints a Dockerfile (the specification for a Docker image) to the\n",
+    "terminal.\n",
+    "\n",
+    "    docker run --rm kaczmarj/neurodocker:v0.3.2 generate \\\n",
+    "               --base debian:stretch --pkg-manager apt \\\n",
+    "               --fsl version=5.0.10 \\\n",
+    "               --miniconda env_name=neuro \\\n",
+    "                           conda_install=\"python=3.6 traits\" \\\n",
+    "                           pip_install=\"nipype\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Build the Docker image\n",
+    "\n",
+    "The Dockerfile can be saved and used to build the Docker image\n",
+    "\n",
+    "    docker run --rm kaczmarj/neurodocker:v0.3.2 generate \\\n",
+    "               --base debian:stretch --pkg-manager apt \\\n",
+    "               --fsl version=5.0.10 \\\n",
+    "               --miniconda env_name=neuro \\\n",
+    "                           conda_install=\"python=3.6 traits\" \\\n",
+    "                           pip_install=\"nipype\" > Dockerfile\n",
+    "\n",
+    "    docker build --tag my_image .\n",
+    "    # or\n",
+    "    docker build --tag my_image - < Dockerfile"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Use NeuroDebian\n",
+    "\n",
+    "This example installs AFNI and ANTs from the NeuroDebian repositories. It also\n",
+    "installs ``git`` and ``vim``.\n",
+    "\n",
+    "    docker run --rm kaczmarj/neurodocker:v0.3.2 generate \\\n",
+    "               --base neurodebian:stretch --pkg-manager apt \\\n",
+    "               --install afni ants git vim\n",
+    "\n",
+    "**Note**: the ``--install`` option will install software using the package manager.\n",
+    "Because the NeuroDebian repositories are enabled in the chosen base image, AFNI\n",
+    "and ANTs may be installed using the package manager. ``git`` and ``vim`` are\n",
+    "available in the default repositories."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Other examples\n",
+    "\n",
+    "Create a container with ``dcm2niix``, Nipype, and jupyter notebook. Install\n",
+    "Miniconda as a non-root user, and activate the Miniconda environment upon\n",
+    "running the container.\n",
+    "\n",
+    "    docker run --rm kaczmarj/neurodocker:v0.3.2 generate \\\n",
+    "               --base centos:7 --pkg-manager yum \\\n",
+    "               --dcm2niix version=master \\\n",
+    "               --user neuro \\\n",
+    "               --miniconda env_name=neuro conda_install=\"jupyter traits nipype\" \\\n",
+    "               > Dockerfile\n",
+    "    docker build --tag my_nipype - < Dockerfile\n",
+    "\n",
+    "Copy local files into a container.\n",
+    "\n",
+    "    docker run --rm kaczmarj/neurodocker:v0.3.2 generate \\\n",
+    "               --base ubuntu:16.04 --pkg-manager apt \\\n",
+    "               --copy relative/path/to/source.txt /absolute/path/to/destination.txt"
+   ]
+  }
+ ],
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