View source for 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 ==
[[Image:Slicer3-xnat.png|thumb|300px|right|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 [http://www.batchmake.org 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?