Slicer3:XCEDE use cases - Revision history

Wjp: /* Slicer use-case #0: Demo we would like to show for BIRN */

2008-08-20T19:44:29Z

Slicer use-case #0: Demo we would like to show for BIRN

Wjp: /* Slicer3 use cases for XCEDE */

2008-08-06T17:40:42Z

Slicer3 use cases for XCEDE

Wjp: /* Overview */

2008-07-28T19:15:15Z

Overview

Wjp: /* Stepping thru details */

2008-07-28T18:02:31Z

Stepping thru details

Wjp: /* Stepping thru details */

2008-07-28T17:59:50Z

Stepping thru details

Wjp: /* Stepping thru details */

2008-07-28T17:57:56Z

Stepping thru details

Wjp: /* Slicer use-case #2: Query Atlas Module */

2008-07-28T17:51:58Z

Slicer use-case #2: Query Atlas Module

Wjp: /* Stepping thru details */

2008-07-28T17:51:07Z

Stepping thru details

Wjp: /* Stepping thru details */

2008-07-28T17:44:20Z

Stepping thru details

Wjp: /* Stepping thru details */

2008-07-28T17:11:44Z

Stepping thru details

@@ Line 7: / Line 7: @@
 ** user provides name/password
 ** user optionally provides tags
 * Slicer closes
 * Web interface to server is used to search by tags
@@ Line 17: / Line 21: @@
 * IGT use-case where multiple investigators contribute data to scene
 * workflow use case where investigator assigns processing tasks to RAs using tags to keep track of processing state
 === Slicer use-case #1: Managing image processing project in a Neuroscience Lab ===

← Older revision		Revision as of 17:40, 6 August 2008
Line 1:		Line 1:
	== Slicer3 use cases for XCEDE ==		== Slicer3 use cases for XCEDE ==
		+
		+	=== Slicer use-case #0: Demo we would like to show for BIRN ===
		+	* Begin with complex scene loaded in slicer (freesurfer, query atlas, fMRI overlay, tractography, and multiple scene snapshots).
		+	* Publish scene to XCEDE compliant web service (initially XNAT, plus HID if possible)
		+	** user provides server base URI or uses default
		+	** user provides name/password
		+	** user optionally provides tags
		+	* Slicer closes
		+	* Web interface to server is used to search by tags
		+	* Clicking MRML download link from web server starts slicer on local machine
		+	* Full scene is restored
		+	* (modify scene, reupload, repeat..)
		+
		+	''Options/extensions:''
		+	* initial scene could have been loaded through web service query based on subject metadata (returning XCAT that is loaded to slicer)
		+	* IGT use-case where multiple investigators contribute data to scene
		+	* workflow use case where investigator assigns processing tasks to RAs using tags to keep track of processing state

@@ Line 157: / Line 157: @@
 *Step0A: Researchers describe FreeSurfer and FIPS datasets for each subject in a study using XCEDE spec.
-*Step0B: Researchers create a notebook describing relevant FIPS and FreeSurfer datasets for each subject in a study.
+*Step0B: Researchers create a notebook referencing relevant FIPS and FreeSurfer datasets for each subject in a study.
 *Step1:  Researchers upload data and description to hosted repository.
 *Step2:  Investigator queries hosted repository for all subjects with a particular diagnosis (SZ) and have a FreeSurfer analysis, and a FIPS analysis for a particular protocol (SIRP).

@@ Line 236: / Line 236: @@
   curl -X GET http://www.myHID.org/...
+'''Response:'''
 --------------------------------------------------------------------
@@ Line 244: / Line 244: @@
   curl –X GET http://www.myHID.org/...
 --------------------------------------------------------------------
-'''Step4.''' Combined results are viewed in the QueryAtlas's ontology- and atlas-based context. Investigator chooses search terms and queries web-based resources for related information. Perhaps all links to data in the notebook populate the QueryAtlas's saved-links menu.
+'''Step4.''' (Inside Slicer) Combined results are viewed in the QueryAtlas's ontology- and atlas-based context. Investigator chooses search terms and queries web-based resources for related information. Perhaps all links to data in the notebook populate the QueryAtlas's saved-links menu.
 --------------------------------------------------------------------
-'''Step5.''' Investigator reviews new search results and saves all references of interest in a local bookmark file for continued study or recommended reading.
+'''Step5.''' (Inside Slicer) Investigator reviews new search results and saves all references of interest in a local bookmark file for continued study or recommended reading.

@@ Line 215: / Line 215: @@
   curl –X PUT -u user:passwd -T MorphologyFunctionNotebook_SIRP.nb http://www.myHID.org/protocols/visit/{path}/MorphologyFunctionNotebook_SIRP.nb?  {all tags from the visit including protocol=SIRP Subject=fbphIIS10056 ...}
-Response: Get back XCEDE XML with new ID.
+'''Response:''' Get back XCEDE XML with new ID.
 --------------------------------------------------------------------

← Older revision		Revision as of 17:57, 28 July 2008
Line 215:		Line 215:
	curl –X PUT -u user:passwd -T MorphologyFunctionNotebook_SIRP.nb http://www.myHID.org/protocols/visit/{path}/MorphologyFunctionNotebook_SIRP.nb? {all tags from the visit including protocol=SIRP Subject=fbphIIS10056 ...}		curl –X PUT -u user:passwd -T MorphologyFunctionNotebook_SIRP.nb http://www.myHID.org/protocols/visit/{path}/MorphologyFunctionNotebook_SIRP.nb? {all tags from the visit including protocol=SIRP Subject=fbphIIS10056 ...}

		+	Response: Get back XCEDE XML with new ID.

	--------------------------------------------------------------------		--------------------------------------------------------------------

← Older revision		Revision as of 17:51, 28 July 2008
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	curl –X POST -u user:passwd -T MorphologyFunctionNotebook_SIRP.nb http://www.myHID.org/protocols/visit/{path}/MorphologyFunctionNotebook_SIRP.nb?		curl –X POST -u user:passwd -T MorphologyFunctionNotebook_SIRP.nb http://www.myHID.org/protocols/visit/{path}/MorphologyFunctionNotebook_SIRP.nb?
		+
		+
		+	'''Response:''' Probably only need an integer back that flags success/failure.

	=== Slicer use-case #3: Qdec Module ===		=== Slicer use-case #3: Qdec Module ===

@@ Line 223: / Line 223: @@
   curl –X GET http://www.myHID.org/visits?project=FBIRN&diagnosis=SZ&protocol=SIRP
-And gets a list or uris as a result result like:
+'''Response:''' Receives back XCEDE XML describing list of uris for appropriate visits and return code; If return code is good, parse XML to get list of uris and display them using some tool or another. Gets a list like:
-  http://central.xnat.org/visit1/fbphIIS10056_SIRP
+  http://www.someHID.org/visit1/fbphIIS10056_SIRP
-  http://central.xnat.org/visit2/fbphIIS10056_SIRP
+  http://www.someHID.org/visit2/fbphIIS10056_SIRP
   ...
-  http://central.xnat.org/visit1/fbphIIS10048_SIRP
+  http://www.otherHID.org/visit1/fbphIIS10048_SIRP
-  http://central.xnat.org/visit2/fbphIIS10048_SIRP
+  http://www.otherHID.org/visit2/fbphIIS10048_SIRP
 Now how will the investigator learn whether both FIPS and FreeSurfer data exist for the first uri?

@@ Line 213: / Line 213: @@
 '''Step1.''' Researchers upload data and description (or notebook) to hosted repository.
-  curl –X PUT -u user:passwd -T MorphologyFunctionNotebook_SIRP.nb http://central.xnat.org/protocols/visit/{path}/MorphologyFunctionNotebook_SIRP.nb?  {all tags from the visit including protocol=SIRP Subject=fbphIIS10056 ...}
+  curl –X PUT -u user:passwd -T MorphologyFunctionNotebook_SIRP.nb http://www.myHID.org/protocols/visit/{path}/MorphologyFunctionNotebook_SIRP.nb?  {all tags from the visit including protocol=SIRP Subject=fbphIIS10056 ...}
@@ Line 221: / Line 221: @@
 '''Step2.''' Investigator queries hosted repository for all subjects with a particular diagnosis (SZ) who have been tested with a particular protocol (SIRP).
-  curl –X GET http://central.xnat.org/visits?project=FBIRN&diagnosis=SZ&protocol=SIRP
+  curl –X GET http://www.myHID.org/visits?project=FBIRN&diagnosis=SZ&protocol=SIRP
 And gets a list or uris as a result result like:
@@ Line 233: / Line 233: @@
 Now how will the investigator learn whether both FIPS and FreeSurfer data exist for the first uri?
-  curl -X GET ...
+  curl -X GET http://www.myHID.org/...
@@ Line 242: / Line 242: @@
 '''Step3.''' Investigator downloads some subset of the datasets in an XCEDE catalog (or notebook?) and opens with Slicer.
 --------------------------------------------------------------------
-'''Step4.''' Combined results are viewed in the QueryAtlas's ontology- and atlas-based context. Investigator chooses search terms and queries web-based resources for related information.
+'''Step4.''' Combined results are viewed in the QueryAtlas's ontology- and atlas-based context. Investigator chooses search terms and queries web-based resources for related information. Perhaps all links to data in the notebook populate the QueryAtlas's saved-links menu.
@@ Line 252: / Line 253: @@
-'''Step5.''' Investigator reviews search results and saves all data of interest in a bookmark file (or in the XCEDE notebook?) for continued study (or recommended reading.
+'''Step5.''' Investigator reviews new search results and saves all references of interest in a local bookmark file for continued study or recommended reading.
@@ Line 258: / Line 259: @@
-'''Step6.''' Investigator publishes notebook containing references to datasets and related resources back to hosted repository.
+'''Step6.''' Investigator also updates a notebook containing additional references to datasets and related resources back to hosted repository.
 === Slicer use-case #3: Qdec Module ===

← Older revision		Revision as of 17:11, 28 July 2008
Line 219:		Line 219:


−	'''Step2.''' Investigator queries hosted repository for all subjects with a particular diagnosis (SZ) ~~and~~ have ~~a FreeSurfer analysis, and a FIPS analysis for~~ a particular protocol (SIRP).	+	'''Step2.''' Investigator queries hosted repository for all subjects with a particular diagnosis (SZ) who have been tested with a particular protocol (SIRP).

	curl –X GET http://central.xnat.org/visits?project=FBIRN&diagnosis=SZ&protocol=SIRP		curl –X GET http://central.xnat.org/visits?project=FBIRN&diagnosis=SZ&protocol=SIRP
−	~~curl -X GET~~

		+	And gets a list or uris as a result result like:
		+
		+	http://central.xnat.org/visit1/fbphIIS10056_SIRP
		+	http://central.xnat.org/visit2/fbphIIS10056_SIRP
		+	...
		+	http://central.xnat.org/visit1/fbphIIS10048_SIRP
		+	http://central.xnat.org/visit2/fbphIIS10048_SIRP
		+
		+	Now how will the investigator learn whether both FIPS and FreeSurfer data exist for the first uri?
		+
		+	curl -X GET ...