Docker container to run generic image-based QC as an XNAT container service

Prerequisites

• XNAT 1.7 or 1.8
• Container service plugin installed (this is done by default in XNAT 1.8)
• Docker installed on XNAT server

Installation instructions

1. Building the data type plugin

   cd plugin ./gradlew jar

2. Copy the plugin to the XNAT plugin directory

   cp build/libs/xnat-imgqc-plugin-0.0.1.jar $XNAT_HOME/plugins

3. Restart the XNAT server

For example on Redhat/Centos sudo systemctl restart tomcat

4. Install the data type

• Log in to XNAT as administrator. From the menu select Administer->Data Types
• Select Set up additional data type
• Select xnat_imgqc:QCData
• Enter ImgQCData for the singular and plural names, otherwise just click Next leaving other options unchanged
• ImgQCData should now be listed in the data types list

5. Install the Docker image

• From the menu select Administer->Plugin Settings
• Select Images and commands
• Select Add new image
• For Image Name enter martincraig/xnat-imgqc. Leave version blank
• Select Pull image

6. Add the command definition if required

Note that there is a bug in some versions of XNAT that means the command definition is not correctly extracted from the Docker image. Under Administer->Plugin Settings, look for ImgQC under Command Configurations. If it is not present you will need to do the following:

• Under Images and Commands expand hidden images
• Find martincraig/xnat-imgqc and click Add Command
• Delete any text, and paste the contents of docker/img_qc_cmd.json into the window
• Click Save command

7. Enable the command for the XNAT server

This can be done under Images and Commands on the Plugin Settings page

8. Enable the command for a project

Select a project and click Project Settings from the menu. The ImgQC command should be listed and can be enabled. Default settings can also be added

9. Run the command

Select an MR session, click Run Container and select ImgQC