Admin UI - Miscellaneous Settings
The "Miscellaneous" tab in the Admin UI has become a holding area for settings that are not easily categorized elsewhere. Some of these settings may move into new tabs as more related functionality appears in future releases of XNAT.
Scan Type Mapping
When sessions are imported into XNAT, their scan types are derived from the DICOM Series Description as entered at the scanner. This can be useful, but it may also contain tiny variations that are no longer relevant to your project. For example, you may want to take all MR scans labeled with some variation of "T1", "MPRAGE", "MPR", or "Structural" and give them all a common label so they can be grouped together in future analysis. Project owners can use the Scan Type Cleanup function to perform this relabeling, when this feature is enabled in your site.
Setting / Property Name | Description | Default |
|---|---|---|
Scan Type Mapping
| This site-wide setting in the Admin UI toggles the availability of the Scan Type Cleanup function for all projects. | Enabled |
Scan Table Settings
These settings customize which columns are displayed in the scan table section of all image session report pages.
Setting / Property Name | Description | Default |
|---|---|---|
Display Series Description
| Displays the "Series Description" column in the scan table listing. By default, this attribute is taken from the DICOM tag (0008,103E) | Enabled |
Display Series Class
| Displays the "Series Class" column in the scan table listing. This is not populated by default from DICOM, but can be added by other processes that perform scan classification. (This is separate from the Scan Type Cleanup function listed above.) | Default |
Recent Data Activity Table Settings
These settings customize columns available in the Recent Data panel on the site home page.
Setting / Property Name | Description | Default |
|---|---|---|
Display Scanner Name
| Displays the "Scanner" column in the recent data table listing. By default, this attribute is taken from the DICOM tag (0008,1010) | Disabled |
Display Experiment Date
| Displays the “Experiment Date” column, which is taken from the DICOM study date (0008,0020) tag | Disabled |
Cross Modality Session Merging
XNAT departs from DICOM in how it classifies image sessions – in XNAT, modality is classified at the session level (i.e. "MR Session", "PET Session"), whereas in DICOM, modality is set on each individual scan series and an image session can easily contain multiple scan modalities. Commonly, this is through the use of a hybrid device such as a PET-MR scanner, which has led to specialized handling of PET-MR sessions in XNAT.
This setting controls session merging behavior, if you are sending scans of a new modality (i.e. a PET scan) to an image session that has already been archived as a different modality (i.e. an MR Session).
Setting / Property Name | Description | Default |
|---|---|---|
Prevent cross-modality post-archive session merger
| When "Enabled", prevents XNAT from merging scans whose modality differs from the archived image session. | Enabled |
Manual QC Action Display
The "Manual QC" is a very common image session assessor whose datatype is enabled by default in XNAT installations, but is not immediately accessible in the XNAT UI. Making this assessor available in the UI involves modifying the Report Actions for each individual image session type, which is a mildly onerous task. This setting provides an easy shortcut to this utility, but does not override any Report Action customizations. So it is conceivable that a site admin could inadvertently add multiple "Add Manual QC" actions by setting this up in multiple places.
Setting / Property Name | Description | Default |
|---|---|---|
Manual QC Actions Menu Item
| When "Enabled", lists "Add QC Entry" as a report action to every image session datatype report page | Disabled |
Development Utilities
This panel contains links to utilities that are most often used by XNAT developers, but can also be used by site administrators as well.
Spawner
XNAT does not react well to YAML syntax errors. Tread cautiously in this control panel.
XNAT Spawner elements control what shows up in the admin UI. If you have customized XNAT and want there to be new administrator options for your customizations, you can add new options by clicking 'Manage Spawner Elements'. Spawner elements are configured using YAML, so some knowledge of YAML is required.
Swagger
Swagger is not a "sandbox" environment. Any REST call (including POST, PUT, or DELETE) made via the Swagger interface will be executed on your server and will modify your site. When they say "Try it out", they mean "Execute this call".
Swagger enables you to directly access elements of the XNAT REST API through the UI that have the prefix "/xapi". If you click the View the Swagger Page, click on the section of the REST API you want to access, and then click on the REST call you want to make, you can then enter any parameters you want and click 'Try it out!' to issue the REST call.
Monitoring
JavaMelody provides built-in application monitoring for your XNAT server instance, including near-real-time monitoring of memory usage and logs of system errors. One useful feature is the ability to inspect and clear system caches to improve performance. The embedded JavaMelody installation in your XNAT comes with its own help documentation, available at {XNAT_SERVER_PATH}/monitoring?resource=help/help.html