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Using XNAT§

  • How to access the servers: See How to log in.
  • Preventing automatic logout: The XNAT server will automatically log you out after a period of inactivity. The remaining time is shown at the top of the screen next to Auto-logout in:. Click renew to reset the timer.

How XNAT organises your data§

  • Projects: Your study has its own XNAT project containing your data. Some multi-centre studies may have more than one XNAT Project.
  • Subjects: Within your project, your data are grouped by Subject (patient). General data about the subject may be stored at the Subject level.
  • Sessions: Your imaging or other acquired data are organised into Sessions (also known as Experiments) which are grouped under the the corresponding subject. A session typically represents a single image acquisition but can contain other related data. A session may contain imaging source data files, metadata, processed data and other files. Sessions can also store non-imaging data, such as questionnaires or clinical trial results.

The XNAT home screen§

The XNAT home screen appears when you log in. You can return to the XNAT home screen at any time by clicking the XNAT logo (top-left of screen).

XNAT Home Page

The XNAT home screen shows:

  • A search panel (top part of page), which allows you to find Projects, Subjects or specified types of sessions (MR, PET, CT etc) by selecting the appropriate tab. You can search for particular items or create tables and spreadsheets from your data. See Searching in XNAT for more information. XNAT Home Page

  • Projects (bottom left of page) is a list of all the projects you have access to. Click on a project name to go to the project report page.

  • Recent Data Activity (bottom-right of page) tells you which of your projects and sessions have recently been modified. Click on a project or session name to go to the project or session page.

Viewing project information§

The project report page is the home page for your project.

To access the project report page:

  • Click on the project name on the XNAT home page to go to your project report page, which is the home page for your project.
  • or navigate to a project from the top menu by selecting Browse > All Projects > (project name)

Project report page§

Project report page

The project report page contains the following parts:

  • Project details

The top panel of the project report page displays project information and settings. The main project details are shown under the Details tab.

The other options Access, Manage and Pipelines are used for advanced project configuration. See Configure XNAT projects for for information.

  • Project contents

The bottom panel shows a table of the subjects and sessions in your project. If sessions are not visible, click the Add Tab button to add a particular type of session to the table. Click on a subject or session name to go to the subject or session report page.

You can show or hide additional data columns in the table. You can also sort or filter the data and export the resulting table as a spreadsheet. See XNAT Data tables and exporting spreadsheets for more information.

  • Project Actions menu

At the right of the page is an Actions menu which contains useful shortcuts

Commonly used items on the actions menu: - Upload Images displays data upload options - see Uploading Data - Add to Favourites will add your project to the Browse > Favourite Projects menu at the top of the screen - Download Images downloads project imaging data - see Downloading data from your project

Other items on the actions menu: - Add allows you to manually creates subjects and sessions. For many projects this will not be required as your uploading process will manage this - see Uploading Data - View Prearchive - not relevant for most projects- see Advanced data import configuration - Download XML downloads the project metadata as an XML file - Manage Files may be used if you wish to store resource files at the project level. In many cases it is more appropriate to store such files under a relevant session, in which case you should navigate to the session first before selecting Manage Files. See Uploading data to your project - Project Settings is for advanced configuration of XNAT plugins (Xsync, Container Service)

Viewing subject information§

The subject report page is the home page for a particular subject. It allows you to view and modify details about that subject and access the associated sessions.

To access a subject report page:

  • From your project home, click the subject name under the Subjects tab at the bottom of the page
  • Alternatively, from the top menu, click Browse > Data > Subjects and select the subject from the list

Subject report page§

Subject report page

The subject report page shows the following:

  • Details shows information (metadata) about this subject. You can modify this information if you have permission using using Edit from the Actions menu on the right.

  • Custom Variable sets (if visible) shows additional information (metadata) about this subject. These are custom data fields specific to your project. You can modify this information if you have permission using using Edit from the Actions menu on the right. The project administrator can add additional custom fields here

  • Experiments shows a list of sessions (also called experiments) for this subject. Click on an experiment name to show the session report page.

  • Actions is a menu containing useful shortcuts:

  • View Subject launches the OHIF Viewer to visualise the subject data
  • Edit is used to modify the subject details
  • View XML displays the subject metadata on screen in XML
  • Download XML downloads the subject metadata as an XML file
  • Manage Files is for storing additional files that relate to the subject but not to any specific imaging sessions. In most cases you should instead store files in a relevant session. You would do this by going to the session and clicking Manage Files from there

Viewing session information§

The session report page is the home page for a session (also known as experiment), which typically represents a data acquisition. A session may contain imaging data, processed data results, and associated data and files.

To view the session report page:

  • From the subject report page for that subject, click the session name under the Experiments list at the bottom of the page
  • Alternatively, from the top menu, click Browse > Data > (Session type) and click on the session label from the list

Session report page§

Session report page

The session report page shows the following:

  • Details shows information (metadata) about this session. You can modify this information if you have permission using using Edit from the Actions menu on the right.

  • Custom Variable sets (if visible) shows additional information (metadata) about this session. These are custom data fields specific to your project. You can modify this information if you have permission using using Edit from the Actions menu on the right. The project administrator can add additional custom fields here

  • Scans shows a list of image scans within this session. Click on a Scan name to show additional scan metadata. DICOM tags can be shown by clicking on the scan and then selecting View DICOM Headers.

  • You can download particular scans by enabling the checkbox next to the desired scans and clicking the Bulk Actions: Download button

  • History Click the [+] button to show details of the creation and changes to this session.

  • Actions is a menu containing useful shortcuts:

  • View Session launches the OHIF Viewer to visualise the session data
  • Download > Download Images allows to to download the images for this session
  • View > XML displays the subject metadata on screen in XML
  • Download > XML downloads the subject metadata as an XML file
  • Manage Files is for storing additional files that relate to the session. See Working with data for more information,

Viewing scan information§

From the session report page you can click on a scan name to show more information about a scan.

Scan details

This information is normally generated by custom upload and processing pipelines.

Viewing DICOM headers for a scan§

You can display the DICOM headers for a scan.

  • View scan information as described above
  • Click on View Dicom Headers at the bottom of the scan information window to display all the DICOM header tags.

DICOM Headers

Note this will show you representative headers for the whole scan and will not show you values that change between slices.