|
|
| (5 intermediate revisions by 2 users not shown) |
| Line 1: |
Line 1: |
| − | == 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/
| |
| − | ** http://sandbox.xnat.org/
| |
| − | | |
| − | == 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
| |
| − | | |
| − | == 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?
| |
