ndreg

Package that performs affine and LDDMM registration easily

Installation

Easy way

Pull image from Docker Hub (link here)

docker pull neurodata/ndreg

Hard way

Build image from Dockerfile

First clone this repository: git clone git@github.com:neurodata/ndreg.git
From inside the ndreg directory: docker build -t ndreg .

Running

In order to use the functionality built into this Docker image, you need to mount your local data volume as follows:

docker run --rm -v /path/to/your/data:/run/data/ -p 8888:8888 neurodata/ndreg

This should print a link to the terminal console that looks like this:

http://0.0.0.0:8888/?token=SOME_TOKEN

Go to this link in your browser by copying and pasting it.

All of the data you mounted should be in the /run/data directory in the Docker image. Keep in mind that anything added to/deleted from that directory is also added to/deleted from the local machine (not just the Docker image)

You can look at the sample notebook in /run/ndreg/Registration package test.ipynb to see how to use the two packages Preprocessor and Registerer