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== Background ==
+
<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [https://www.slicer.org/wiki/Slicer3:XNAT here]</font></big>
 
 
* 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?
 

Latest revision as of 18:07, 10 July 2017

Home < Slicer3:XNAT

Note: We are migrating this content to the slicer.org domain - The newer page is here