XNAT 1.8.0 Release Notes

These release notes include all updates that were made since the release of XNAT 1.7.6, the last public release. This includes changes made for XNAT 1.7.7, which was an internal-only release where most of the code changes do not have corresponding JIRA tickets. These release notes offer some additional notes on new features and bugfixes based on those updates.

Browser Support

As of XNAT 1.8, we no longer support running XNAT on any version of Internet Explorer, which has been deprecated by Microsoft and will stop receiving security updates in 2021. Microsoft Edge and all other modern browsers (Firefox, Chrome, et al) are supported.

XNAT Event Service

XNAT 1.8 ships with a fully rebuilt means of automating tasks in relation to filterable events in XNAT. This is a powerful new feature, and one that becomes more powerful when combined with the Container Service.

See: Using the XNAT Event Service

XNAT Architecture

Modernized XNAT Components

XNAT 1.8 is now built on Java 8 and requires PostgreSQL 9.6 – with PostgreSQL 10 or higher recommended. In the UI, the jQuery library and related libraries have been updated to version 3.5.1.

See: Prerequisites for Installing XNAT

Other Architectural Improvements and Bug Fixes

Among other architectural improvements, XNAT 1.8 offers improved support for Multi-Node XNAT configurations, which help distribute traffic and server load on very large systems such as CNDA. Additional bugfixes addressed issues with LDAP logins and database upgrading from older versions of XNAT.

• XNAT-3893: Migrate to a Gradle-based XNAT builder
• XNAT-5202: Address restarting issues in Vagrant XNAT builds
• XNAT-6076: Fix Spawner initialization in multinode deployments
• XNAT-6416: Fix Postgres issue during upgrade from 1.7.6 and lower
• XNAT-6417: Bugfix for shadow server deployments
• XNAT-6452 and XNAT-6601: Bugfixes to support LDAP and other remote authentication methods
• XNAT-6634: Add support for LDAP-style authentication headers

Image Viewing is Plugin-Enabled

XNAT supports two separate image viewing plugins, and XNAT administrators can choose to install one or both depending on their needs.

• The XNAT-OHIF Image Viewer is highly recommended for its ability to support segmentations and annotations, as well as receiving ongoing support and development
• The Legacy XNAT Image Viewer has been deprecated and removed from core XNAT, but can still be run as a plugin. Its primary advantage is an ability to view NIFTI images

Resource Management

New Feature: Triaging Custom Resource Uploads

XNAT 1.8 introduces improvements to the Custom Resource Uploader workflow, by adding the additional concept of allowing project owners to send incoming resource files to a "Triage" space where they can be proofed before they are added to the project. See: Using the Resource File Quarantine

Other Resource Management Improvements and Bug Fixes

XNAT 1.8 includes a number of bugfixes for the catalog service, as well as handling assessor resources – particularly those created via the REST API. Fixes include:

• XNAT-4653 and XNAT-6458: Restore resource file manager UI for shared subjects 
• XNAT-6079: Fix an error with dropped files when handling gzipped resources
• XNAT-6400: Enable file level metadata in catalog service
• XNAT-6421: Bugfix for project routing in default catalog service
• XNAT-6429: and XNAT-6444: Improve support for assessor resources re: IN or OUT specification
• XNAT-6431: Bugfix for workflow tracking when clicking "upload additional files"
• XNAT-6432: Prevent unnecessary catalog refresh during Upload Additional Files workflows 
• XNAT-6442: Restore ability to delete resource files with spaces in the name
• XNAT-6455: Fix API handling for assessor resources
• XNAT-6465: Fix rare workflow conflicts for Autorun resource creation
• XNAT-6497: Enable compressed file handling via catalog service
• XNAT-6543: Address NPE when creating an experiment resource without XML

Datatype Management

Enabling Searchable Scan Listings

Enabling image scan datatypes in XNAT has long been fraught with bad or strange behavior, and admins were often cautioned not to do it. XNAT 1.8 now offers full support for enabling scan listings. This improvement has a cascading positive benefit when used with the Container Service and Batch Launch Plugin, allowing users to launch containers (such as dcm2niix) in bulk on scan data across their project or across search listings.

See: Using the Batch Launch Plugin with the Container Service

ROI Collection Added to Core XNAT Data Types

The ROI Collection datatype plugin was a required prerequisite for running the XNAT-OHIF Viewer Plugin. This datatype has now been moved into the core XNAT data model, which obviates the need to re-install it via the datatype plugin. If installed, the ROI Collection datatype plugin can be safely removed.

Other Datatype Management Improvements and Bug Fixes

XNAT 1.8 includes a series of minor bugfixes related to datatype management, including unintended behavior when removing elementSecurity entries. Fixes include: 

• XNAT-6412: Allow removal of elementSecurity entry on datatypes
• XNAT-6482: Fix session display issues when enabling scan datatypes
• XNAT-6490: Allow creation of an XNAT image session from RT series
• XNAT-6508: Allow XSync to work with ROI Collection data

Archiving

Enabling Custom DICOM Project Routing Rules (Without a Plugin)

XNAT 1.8 resurrects and empowers the mostly defunct dicom-project.rules method of specifying custom DICOM fields to query to determine project routing during the session-building and archiving process. With this method now positioned at the top of the logical stack, XNAT 1.8 makes it possible for a site administrator to set these rules on their site via the API or the Site Admin UI. 

See: 

• XNAT-6450: Allow customization of routing rules without a plugin
• Documentation: How XNAT Scans DICOM to Map to Project/Subject/Session

Generating Scan Snapshots and Montages on the Fly

XNAT 1.8 rebuilt the snapshot generation service, and made it available as a core service rather than relying on the Autorun pipeline. This new service functions on the fly, which adds incremental performance benefits to the scan archiving process. It also makes it easy for users to generate their own snapshots, including single-slice views and montage views.

See: Generating Scan Snapshots and Montages in XNAT

Enhancements to Anonymization

XNAT 1.8 now uses version 6.3 of the DicomEdit6 library, providing new capabilities, including the ability to mask regions of pixel data that have burned-in PHI.

See: DicomEdit 6.3 Language Reference

Other Session Archiving Improvements and Bug Fixes

Among other improvements related to session archiving, XNAT 1.8 resolves a bug that prevented Mammogram data from being archived properly in some cases.

• XNAT-5460: Use LE-Explicit rather than LE-Implicit transfer syntax when necessary
• XNAT-5496: Fix bug preventing mammogram merging behavior
• XNAT-6123: Performance fix for subject metadata updating

XNAT Admin Permissions

Rationalized Admin Access Permissions

For a long time, it was possible in XNAT for a site administrator to not grant themselves access to all project data. However, as site administrators, they always have the ability to toggle that all-data-access switch back on at their leisure. This created a phantom role of the "data-blind site admin" whose existence depended entirely on the chivalry of the person in that role. This was not a sustainable practice, and also created logistical nightmares when coding around "admin" permissions as related to the hundreds and hundreds of API endpoints in XNAT.

In XNAT 1.8 and moving forward, a site administrator will always be granted access to all project data.

Other Administrative Improvements and Bug Fixes

XNAT 1.8 resolved a series of minor usability issues related to the Admin UI and Project Admin UI, including the ability to enable and disable Series Import Filters.

See: 

• XNAT-5841: Make unsupported user admin status more clear
• XNAT-5843: Use consistent views for history item listings in Admin UI

Security Fixes

A number of security issues were addressed in XNAT 1.8.0. Affected areas include project resources, alias tokens, and cross-site scripting.

View All Improvements and Bug Fixes in JIRA

Improved Asynchronous Handling of Selected Workflows

XNAT 1.8 introduces the new "Activity" tab, which appears on the bottom of the screen to track asynchronous processes in the UI. Examples of newly asynchronous processes include the Compressed Image Uploader, the Review and Archive feature within the Prearchive, and Container launches.

Other UI Improvements and Bug Fixes

XNAT 1.8 addressed a series of minor UI behaviors and rendering issues, including the following: 

• XNAT-3274: Remove Add Experiment link from Project Actions box for users below Member privileges
• XNAT-5786: Address scalability of custom project listings when accessed by multiple users
• XNAT-6060: Increased size of the "Title" field for Investigators
• XNAT-6063: Fix rendering of special characters in report pages
• XNAT-6121: Fix breadcrumbs on report pages outside project scope
• XNAT-6145: Fix email regex validation
• XNAT-6371: Javascript API fix for URL parameters 
• XNAT-6398: Increase size of Scan column on session listings
• XNAT-6437: Support longer notes on scan report pages 
• XNAT-6447: Remove extraneous clicks from Upload Additional Files workflows 
• XNAT-6653: Fix QC summary on session page  

Other Backend Improvements and Bug Fixes

XNAT 1.8 addressed a series of minor backend behaviors, including the following:

• XNAT-5498: Content-type bugfix for alias tokens
• XNAT-6381: Address intermittent user permissions issues
• XNAT-6404: Address inability to download files from projects whose project ID is made up only of numbers and starts with a zero
• XNAT-6423: Permissions check bugfix on certain assessor URIs
• XNAT-6424: Fix performance issue related to backup directories when uploading scans in sequence
• XNAT-6645 and XNAT-6682: Bugfixes for XSync behavior

Known Issues in XNAT 1.8

There are several issues and improvements on tap. These are a selection of higher priority known issues.