XNAT User Guide Overview
XNAT: an extensible open-source imaging informatics software platform dedicated to imaging-based research. XNAT is a Tomcat web application with a Postgresql database backend. Users interact with XNAT via a web user interface.
Docker: Docker is a technology that enables software and servers to be packaged into lightweight virtual machines - the software, operating system and dependencies are packaged into 'images' and these images can be run in 'containers'.
XNAT and Permissions:
Every user of XNAT has different permissions. Each user will have different access to projects and ability to create or delete data in XNAT.
Each project can be Private, Protected or Public. If a User has access to a project, they will be either:
- Owners - can add and delete data, and modify the Project settings.
- Members - can only add and download data.
- Collaborators - can only download data.
Data in XNAT is stored in the Archive.
Data is organised into a hierarchical structure within XNAT.
Project -> Subject (patient) -> Experiments -> Session such as Imaging session, or other Subject Assessments
A project contains one or more subjects which usually represent individual patients. Subjects cannot exist outside a project. Each subject can have one or more experiments. The term experiment is used in the XNAT world for any event that acquires or produces data. One particular type of experiment is an imaging session which for instance can contains CT, MR, or PET scans. Other types of experiments describe assessments, non-imaging sessions, and other custom experiments. For more information have a look at the XNAT documentation.
Within this documentation we use a simplified hierarchy:
Project -> Subject -> Session
In this context, we will refer to Assessors as forms - for example, Facility Questionnaire Form, and Benchmark QC form. These are stored at the subject-level. Outline Review forms belong to the corresponding session.
Projects: data in XNAT is organized in Projects. Projects can be Private, Protected, or Public:
Private: Only users with access can see the project and know it exists.
Protected: The Project is visible to all Users on the XNAT homepage, but only member/owners of the project can access it.
Public: All the Users of XNAT can access the project.
Once you are logged into XNAT you can navigate to the home-page by clicking on the XNAT-icon in the top left-hand corner.
The homepage has four main components:
- Top: The bar for general navigation, administration (if given appropriate rights), and help.
- Middle: The search area with the tabs called Subjects, MR, PET, and CT allows you to search for data within these categories.
- Bottom left: A list of projects.
- Bottom right: A list of recent data activity.
Clicking on a project on the left will take you to the project page.
The project page provides tabs which provide access to project related settings such as access control, plugin related management, and pipeline settings. Below this you will find a list of subjects included in this project. You can add extra tabs to the table (for example with MR sessions) by clicking on ‘Add Tab’. A drop-down menu with additional tables will appear. You can view the details of each subject or session by clicking on the link in the Subject column.
The Subject page (you will get here by clicking on a subject) lists the sessions and demographic information related to that subject.
The session page gives detailed information about this session which may contain multiple items. CT images and corresponding RT-structures are listed under scans. Assessments of this session appear at the bottom. In this example you see that the RT Struct files was processed into a ROI Collection.