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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
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| − | * Sample XNAT sites:
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| − | ** http://www.oasis-brains.org
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| − | ** http://iaclin2.wustl.edu/mbdr
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| − | ** http://yaz.bwh.harvard.edu:8080/xnat/ (not working: being used to debug Rocks-based install)
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| − | ** http://yaz.bwh.harvard.edu:8080/xnat2/ (does work; manual install)
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| − | ** http://sandbox.xnat.org/
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| − | | |
| − | == Existing Slicer3 Interface == | |
| − | [[Image:Slicer3-xnat.png|thumb|300px|right|Illustration of download process]]
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| − | Basic steps:
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| − | * Browse to the desired image data set
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| − | * Select Download Images
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| − | * Pick which images you want
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| − | * Select the filetype as "xar (3D Slicer)"
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| − | * When the browser asks what to do with the file, select Slicer3 as the application (browse to where the program is installed).
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| − | * Once downloaded, Slicer will look in the file and offer to load the images.
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| − | | |
| − | Planned improvements:
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| − | * Fundamental goals for this project:
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| − | ** is to be able to upload raw data into the database (core xnat feature)
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| − | ** download selected datasets to slicer (see above)
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| − | ** run analysis routines in slicer
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| − | ** upload the results linked back to original data
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| − | * Further nice-to-have goals:
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| − | ** use XNAT as an optional back end for the integration of [http://www.batchmake.org BatchMake] for population processing and parameter space exploration
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| − | ** upload analysis results (numerical values) to database for plotting and other analysis
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| − | | |
| − | == Installation ==
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| − | | |
| − | Options:
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| − | * instructions on http://xnat.org
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| − | | |
| − | * use the BIRN ROCKS installer (contact BIRN-CC via http://www.nbirn.net)
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| − | | |
| − | * use the xnat installer script from Gabriele Fariello (fariello at fas.harvard.edu)
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| − | ** this works for some linux distributions (Red Hat and probably Ubuntu)
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| − | ** you must have Sun Java installed (not the gnu version)
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| − | ** best to use this installer on a fresh machine
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| − | ** apt-get of postgres may hang waiting for you to press 'Y'
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| − | | |
| − | == Tests ==
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| − | | |
| − | Get the xnat webservices command line tools from http://www.xnat.org/tools.html#
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| − | ArcGet -host www.oasis-brains.org -u guest -p guest -s OAS1_0001_MR1 | |
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| − | == Further XCEDE Integration ==
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| − | | |
| − | [[Slicer3:XCEDE_use_cases]]
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| − | | |
| − | == User Requests ==
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| − | | |
| − | Potential users of this project, please list feature requests and/or proposed use scenarios in this section.
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| − | | |
| − | * How is patient deidentification handled in XNAT?
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