XNAT

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Welcome to the XNAT information website. We installed two XNAT (http://www.xnat.org) services for two separate projects. For better management we have one information page for both of these services. We offer the following services which this website further describes:

  • BIGR-XNAT: Service for the BioMedBridges project on https://bigr-xnat.erasmusmc.nl . Each user can, after registration, download data for projects in which he is enrolled. Upload data may also be possible on request.
  • BMIA-XNAT: Service for the CTMM TraIT project on https://xnat.bmia.nl. Primarily for participants in CTMM projects.

These services are only meant for storage of properly anonymised research data related to medical imaging. Proper anonymisation is the responsibility of the user who uploads data.

XNAT Meeting 2015

On 22 and 23 September 2015 an XNAT meeting is organised in the Erasmus MC. This meeting is aimed at users and developers of systems which interact with XNAT or XNAT itself. The format of this meeting will be a hackathon and is aimed at being productive and building a national XNAT developers network. Read for more information XnatMeeting2015.

Exercise

For the BioMedBridges workshop at the BioMedBridges Symposium in November in Hinxton, we made an introductory exercise for new users. It is available at: XNAT.pdf.

Note that the XNAT instance to which is linked to in the exercise may not be online. Before the workshop or other meetings for which we intend to use the exercise, we create several virtual machines beforehand and we will handout the ip-addressed then.

Quick start guide

The official XNAT user guide can be found on: https://wiki.xnat.org/display/XNAT16/2.+User+Documentation. Most information can be found in their user guide. As a quick start guide, this wiki provides a summary of the most relevant points of their documentation, and linking to specific XNAT webpages for more information. Furthermore, several examples and configurations are given.

For testing the project Testsandbox is available. This public project can be used to checkout and try XNAT for viewing and downloading data. If you just want to test XNAT, you can create an account and upload data to this project. This is to prevent that a lot of testprojects are created. For uploading, you have to request access using the registration procedure; see XNAT: Quick Start Guide.

More information about installing XNAT on a new machine/server can be found on: Installation. This is only for administrators that would like to install a new XNAT service. New users that would like to use the two websites above, the XNAT Installation page is not relevant.

Public imaging dataset

An example set of anonyized medical images for testing is available at: ANONYMIZ.zip. A smaller resampled version is available here: ANONYMIZ_resampled.zip.

Contact information

Acknowledgements

BioMedBridges
CTMM

The bigr-xnat service has been setup with support of the BioMedBridges project (http://www.biomedbridges.eu), funded by the European Commission within Research Infrastructures of the FP7 Capacities Specific Programme, grant agreement number 284209.

The bmia-xnat service has been setup with support of the CTMM TraIT project (http://www.ctmm-trait.nl).

Links/references

XNAT instance for BIGR/ErasmusMC: https://bigr-xnat.erasmusmc.nl

XNAT instance for TraIT/CTMM: https://xnat.bmia.nl.

Home page of XNAT: http://www.xnat.org

User documentation: https://wiki.xnat.org/display/XNAT16/2.+User+Documentation