Slicer3:XNAT

Background

• XNAT is available at http://www.xnat.org
• Sample XNAT sites:
  • http://www.oasis-brains.org
  • http://iaclin2.wustl.edu/mbdr
  • http://yaz.bwh.harvard.edu:8080/xnat/ (not working: being used to debug Rocks-based install)
  • http://yaz.bwh.harvard.edu:8080/xnat2/ (does work; manual install)
  • http://sandbox.xnat.org/

Existing Slicer3 Interface

Illustration of download process

Basic steps:

• Browse to the desired image data set
• Select Download Images
• Pick which images you want
• Select the filetype as "xar (3D Slicer)"
• When the browser asks what to do with the file, select Slicer3 as the application (browse to where the program is installed).
• Once downloaded, Slicer will look in the file and offer to load the images.

Planned improvements:

• Fundamental goals for this project:
  • is to be able to upload raw data into the database (core xnat feature)
  • download selected datasets to slicer (see above)
  • run analysis routines in slicer
  • upload the results linked back to original data
• Further nice-to-have goals:
  • use XNAT as an optional back end for the integration of BatchMake for population processing and parameter space exploration
  • upload analysis results (numerical values) to database for plotting and other analysis

Installation

Options:

• instructions on http://xnat.org

• use the BIRN ROCKS installer (contact BIRN-CC via http://www.nbirn.net)

• use the xnat installer script from Gabriele Fariello (fariello at fas.harvard.edu)
  • this works for some linux distributions (Red Hat and probably Ubuntu)
  • you must have Sun Java installed (not the gnu version)
  • best to use this installer on a fresh machine
  • apt-get of postgres may hang waiting for you to press 'Y'

Tests

Get the xnat webservices command line tools from http://www.xnat.org/tools.html#

ArcGet -host www.oasis-brains.org -u guest -p guest -s OAS1_0001_MR1

Further XCEDE Integration

Slicer3:XCEDE_use_cases

User Requests

Potential users of this project, please list feature requests and/or proposed use scenarios in this section.

• How is patient deidentification handled in XNAT?