Introduction

As part of the MEDICSS summer school, we provide the cloud-based infrastructure for the students to run XNAT and the imaging containers. However, if you would like to try this out on your own, please find the instructions below.

Requirements

You will need to have access to an AWS account. Keep in mind that setting up this infrastructure comes with a cost. Take a look a the cost estimates before building this infrastructure.

Setting up the cloud infrastrucutre

You can find all the required scripts for setting this up at the UCL MIRSG XNAT AWS repository. Please clone the repository and read the instructions on how to build carefully

We use Terraform to create all the cloud infrastructure needed for this project, and Ansible to provision the working machines and install XNAT and all the necessary dependencies.

Setting up XNAT

Run the ./install_xnat.sh script and follow the instructions mentioned in the README. These instructions tell you how to obtain admin access to the XNAT. Before you run any containers or event services in the project as is mentioned in the processing section, make sure that these containers are enabled in the Administrator section.

  1. In the top menu, go to Administer->Plugin Settings
  2. In the Plugin Settings menu, click on Command Configurations and enable all of the commands, or the ones you wish to use.
  3. To enable the Event Service, in the top menu, go to Administer->Event Service and turn on the Enable Event Service button.

Appstream

We are working on setting up remote Linux desktops using Appstream 2.0 so that if you want to view the images and results, you don’t have to download them out of the cloud and incur additional cost. You are asked about this when you set up the infrastructure with the terraform apply command. For the time being, click on false, as this feature is not quite ready.