Computing

XNAT is an open-source imaging informatics software platform dedicated to helping with imaging-based research. XNAT’s core functions manage importing, archiving, processing and securely distributing imaging and related study data.

CfN manages an XNAT server that is connected to the CfN cluster. The server URL:

http://picsl-xnat.uphs.upenn.edu/

For some functions on the XNAT server, your browser must have Java enabled to work with the xnat service. However since Java support is being phased out in major browsers, functionality is being transferred to desktop tools by the XNAT team.

The XNAT Wiki has documentation

The XNAT data archive is stored on the /data/tesla-data volume, and is directly accessible with read-only permissions on the cluster at /data/XNAT. This allows direct processing from the cluster of data stored within XNAT.

Individual project directories are readable only by members of a linux group for lab/project members. If you need to be added to the appropriate group, please tell the admins.

XNAT can also be setup to run 'pipelines', which are collections of scripts and processing steps that can be launched and monitored from the XNAT web interface. Please contact the admins for details.

User logins are separate from CfN cluster logins. Please connect the admins for more information.

XNAT organizes data by Project. Each Project has private control of its data and a user must be granted access to a Project to view or edit data.

When data is “in Prearchive”, it means the data has been received and stored by the XNAT system, but it is in a special holding state and has not been fully integrated into a Project. It has not been fully entered into the XNAT database. The Prearchive is a useful holding place for data so it can be reviewed by a Project member and have Subject and Session labels changed as necessary (see below).

When data is “moved to Archive” in XNAT, it means the data has been fully integrated into the XNAT database as part of a Project. It is now viewable and actionable from the Project's page in the web interface.

To manually upload data, use the desktop tool XNAT Upload Assistant. This program runs on your local machine.

For the Upload Assistant setup:

server: http://picsl-xnat.uphs.upenn.edu
username: your XNAT username (probably the same as you cluster username, but may not be)
password: you XNAT password

XNAT can receive data directly from PACS and from the Stellar-Chance research scanner. Please contact the admins for details.