Slicer3:XNAT - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T18:07:26Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Marianna: Protected "Slicer3:XNAT" [edit=sysop:move=sysop]

2008-05-20T20:04:37Z

Protected "Slicer3:XNAT" [edit=sysop:move=sysop]

Marianna: Replacing page with ''''Note:''' We are migrating this content to the slicer.org domain - The newer page is [http://www.slicer.org/slicerWiki/index.php/Slicer3:XNAT here]...'

2008-05-20T20:04:25Z

Replacing page with '<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [http://www.slicer.org/slicerWiki/index.php/Slicer3:XNAT here]...'

Pieper: /* User Requests */

2007-09-26T14:16:08Z

User Requests

Pieper: /* Slicer3 Interface */

2007-09-26T14:15:26Z

Slicer3 Interface

Pieper: /* Background */

2007-08-24T15:35:55Z

Background

Pieper: /* User Requests */

2007-07-13T19:29:40Z

User Requests

Pieper: /* Background */

2007-07-13T15:25:52Z

Background

Pieper: /* Tests */

2007-07-13T14:36:10Z

Tests

Pieper: /* Slicer3 Interface */

2007-07-13T14:35:23Z

Slicer3 Interface

← Older revision		Revision as of 18:07, 10 July 2017
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−	<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [~~http~~://www.slicer.org/~~slicerWiki/index.php~~/Slicer3:XNAT here]</font></big>	+	<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>

← Older revision		Revision as of 20:04, 20 May 2008
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−	~~== Background ==~~	+	<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [http://www.slicer.org/slicerWiki/index.php/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?

← Older revision		Revision as of 14:16, 26 September 2007
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	ArcGet -host www.oasis-brains.org -u guest -p guest -s OAS1_0001_MR1		ArcGet -host www.oasis-brains.org -u guest -p guest -s OAS1_0001_MR1
		+
		+	== Further XCEDE Integration ==
		+
		+	[[Slicer3:XCEDE_use_cases]]

	== User Requests ==		== User Requests ==

@@ Line 9: / Line 9: @@
 ** http://sandbox.xnat.org/
-== Slicer3 Interface ==
+== Existing Slicer3 Interface ==
 [[Image:Slicer3-xnat.png|thumb|300px|right|Illustration of download process]]
 Basic steps:

@@ Line 5: / Line 5: @@
 ** http://www.oasis-brains.org
 ** http://iaclin2.wustl.edu/mbdr
-** http://yaz.bwh.harvard.edu:8080/xnat/
+** http://yaz.bwh.harvard.edu:8080/xnat/ (not working: being used to debug Rocks-based install)
 ** http://sandbox.xnat.org/

← Older revision	Revision as of 20:04, 20 May 2008
(No difference)

← Older revision		Revision as of 19:29, 13 July 2007
Line 52:		Line 52:

	Potential users of this project, please list feature requests and/or proposed use scenarios in this section.		Potential users of this project, please list feature requests and/or proposed use scenarios in this section.
		+
		+	* How is patient deidentification handled in XNAT?

← Older revision		Revision as of 14:36, 13 July 2007
Line 47:		Line 47:

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

@@ Line 17: / Line 17: @@
 * Once downloaded, Slicer will look in the file and offer to load the images.
+Planned improvements:
 == Installation ==