Add description and docker instructions at the top

Author: binarybottle

install/neurodocker.sh

@@ -1,5 +1,48 @@
 #!/bin/bash
 
+###############################################################################
+# Generate a Dockerfile for building a Mindboggle container (http://mindboggle.info).
+# The Dockerfile installs most of Mindboggle's dependencies,
+# including preprocessing software packages FreeSurfer and ANTs,
+# and visualization software roygbiv.
+#
+# Steps:
+#
+# Set up neurodebian and miniconda, and install conda packages.
+# Install FreeSurfer and ANTS.
+# Install Mindboggle templates from the Open Science Framework.
+# Install Mindboggle.
+# Install roygbiv for output visualization.
+#
+# Build the docker image:
+# docker build -t mindboggle -f Dockerfile.mindboggle.complete .
+#
+# Push to Docker hub:
+# (https://docs.docker.com/docker-cloud/builds/push-images/)
+# export DOCKER_ID_USER="nipy"
+# docker login
+# docker tag mindboggle nipy/mindboggle
+# docker push nipy/mindboggle
+#
+# Pull from Docker hub:
+# docker pull nipy/mindboggle
+#
+# In the following, the Docker container can be the original (mindboggle)
+# or the pulled version (nipy/mindboggle), and is given access to /Users/arno
+# on the host machine.
+#
+# Enter the bash shell of the Docker container, and add port mappings:
+# docker run --rm -ti -v /Users/arno:/home/jovyan/work -p 8888:8888 -p 5000:5000 nipy/mindboggle bash
+#
+# Run the Docker container as an executable (variables set for clarity):
+# HOST=/Users/binarybottle # path on host to access input and output
+# DOCK=/home/jovyan/work # path to HOST from Docker container
+# IMAGE=$DOCK/example_mri_data/T1.nii.gz # input image (from container)
+# ID=arno # ID for brain image
+# OUT=$DOCK/mindboggle123_output # '--output $OUT' is OPTIONAL
+# docker run --rm -ti -v $HOST:/home/jovyan/work nipy/mindboggle $IMAGE --id $ID --out $OUT
+###############################################################################
+
 # Generate a dockerfile for building a mindboggle container
 docker run --rm kaczmarj/neurodocker:0.4.1 generate docker \
   --base neurodebian:stretch \