Modules:EMSegment-TemplateBuilder-3.4 - Revision history

Belhachemi: moved Modules:EMSegment-TemplateBuilder to Modules:EMSegment-TemplateBuilder-3.4: Refactoring the EM Wiki Pages

2010-08-19T15:09:17Z

moved Modules:EMSegment-TemplateBuilder to Modules:EMSegment-TemplateBuilder-3.4: Refactoring the EM Wiki Pages

Nicole: /* Source code & documentation */

2010-01-15T22:05:47Z

Source code & documentation

Marianna at 19:26, 26 May 2009

2009-05-26T19:26:57Z

Yumin at 16:25, 19 March 2009

2009-03-19T16:25:21Z

Yumin at 16:16, 19 March 2009

2009-03-19T16:16:05Z

Yumin at 16:06, 19 March 2009

2009-03-19T16:06:31Z

Yumin at 13:46, 17 March 2009

2009-03-17T13:46:29Z

Yumin: /* General Information */

2009-03-17T13:30:55Z

General Information

Yumin at 21:06, 16 March 2009

2009-03-16T21:06:51Z

Yumin: New page: Return to Slicer 3.4 Documentation NOTOC ===Module Name=== EM Segment Template Builder {| |Caption 1 |[[Image:screensh...

2009-03-16T21:03:53Z

New page: Return to Slicer 3.4 Documentation __NOTOC__ ===Module Name=== EM Segment Template Builder {| |thumb|280px|Caption 1 |[[Image:screensh...

New page

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__NOTOC__
===Module Name===
EM Segment Template Builder

{|
|[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive or CLI

Category: Base or (Filtering, Registration, ''etc.'')

===Authors, Collaborators & Contact===
* Author1: Affiliation & logo, if desired
* Contributor1: Affiliation & logo, if desired
* Contributor2: Affiliation & logo, if desired
* Contact: name, email

===Module Description===
Overview of what the module does goes here.

== Usage ==

===Examples, Use Cases & Tutorials===

* Note use cases for which this module is especially appropriate, and/or link to examples.
* Link to examples of the module's use
* Link to any existing tutorials

===Quick Tour of Features and Use===
List all the panels in your interface, their features, what they mean, and how to use them. For instance:

* '''Input panel:'''
* '''Parameters panel:'''
* '''Output panel:'''
* '''Viewing panel:'''

== Development ==

===Dependencies===

Other modules or packages that are required for this module's use.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following [http://viewvc.slicer.org/viewcvs.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

@@ Line 101: / Line 101: @@
 [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ Links] for the module.
 *[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]
-*API: [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentMRMLManager.html MRML Manager] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentLogic.html Module Logic] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentGUI.html Module GUI]
+*API: [http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkEMSegmentMRMLManager.html MRML Manager] | [http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkEMSegmentLogic.html Module Logic] | [http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkEMSegmentGUI.html Module GUI]
 == More Information ==

@@ Line 53: / Line 53: @@
 ===Quick Tour of Features and Use===
-====Steps in the Workflow Wizard====
+There is a [[Modules:EMSegment-TemplateBuilder:EMSegment-TemplateBuilder-Steps | step-by-step instruction]] with screen shots to describe the Workflow Wizard interface.
 *1/9 Define Parameters Set: Select parameter set or create new parameters
 *2/9 Define Hierarchy: Define a hierarchy of anatomical structures
@@ Line 84: / Line 86: @@
 Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.
 ===Usability issues===
@@ Line 99: / Line 99: @@
 *[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]
 *API: [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentMRMLManager.html MRML Manager] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentLogic.html Module Logic] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentGUI.html Module GUI]
 == More Information ==

@@ Line 29: / Line 29: @@
 == Usage ==
-The purpose of the module is to configure the algorithm to automatically segment anatomical structures in medical images. First the user has to specify parameters defining the image protocol and the anatomical structures of interests. This process results in a template that the module uses to automatically segment large data sets. The template is composed of atlas data and a
+The purpose of the module is to configure the algorithm to automatically segment anatomical structures in medical images. First the user has to specify parameters defining the image protocol and the anatomical structures of interests. This process results in a template that the module uses to automatically segment large data sets. The template is composed of atlas data and a non-trivial collection of parameters for the EMSegment algorithm.
 Once the parameters are specified, the target images are segmented
@@ Line 44: / Line 43: @@
 ===Examples, Use Cases & Tutorials===
-* Note use cases for which this module is especially appropriate, and/or link to examples.
+These slides and data describe the Slicer3 implementation of all three EMSegment modules and demonstrate their use.  A recent (later than 7Jan08) version of Slicer3 is required to run the test data.
-* Link to examples of the module's use
-* Link to any existing tutorials
+[[Media:EMSegTutorial-AHM2008.ppt | Tutorial Slides]] - [[Media:EMSegTutorial-AHM2008.zip | Tutorial Data]]
 ===Quick Tour of Features and Use===
@@ Line 99: / Line 102: @@
 == More Information ==
 *For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]
 *The old [[Modules:EM-Segmenter-Documentation:FAQ |EMSegmenter FAQ]] contains frequently asked questions about the EMSegment interfaces in Slicer3.

@@ Line 5: / Line 5: @@
 {|
-|[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
+|[[Image:EMSegment-Workflow.png|thumb|580px|EM Segment Workflow]]
-|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
+|[[Image:EMSegment-Template.png|thumb|580px|EM Segment Template Builder GUI and EM Segment Result]]
 |}
@@ Line 91: / Line 90: @@
 Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.
 ===Source code & documentation===
@@ Line 103: / Line 99: @@
 == More Information ==
-For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]
+*For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]
 ===Acknowledgment===
 Funding for the EMSegmenter module was provided by NAMIC.

← Older revision	Revision as of 15:09, 19 August 2010
(No difference)

@@ Line 1: / Line 1: @@
 [[Documentation-3.4|Return to Slicer 3.4 Documentation]]
 __NOTOC__
 ===Module Name===

@@ Line 26: / Line 26: @@
 ===Module Description===
-The EMSegment template builder module is the primary Slicer3 interface to the EMSegment algorithm.  The target audience for this module is someone familiar with brain atlases and tissue labels, not a computer scientist.  It allows the user to configure the algorithm---step-by-step---to a variety of imaging protocols and anatomical structures, and then apply the algorithm to segment data.  Configuration settings are stored in an EMSegment parameters node in the Slicer3 MRML tree.  These settings can be saved and later applied to new data via any of the EMSegment interfaces within Slicer3 or the command-line EMSegment executable.
+The EMSegment template builder module is the primary Slicer3 interface to the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. The target audience for this module is someone familiar with brain atlases and tissue labels, not a computer scientist.  It allows the user to configure the algorithm---step-by-step---to a variety of imaging protocols and anatomical structures, and then apply the algorithm to segment data.  Configuration settings are stored in an EMSegment parameters node in the Slicer3 MRML tree.  These settings can be saved and later applied to new data via any of the EMSegment interfaces within Slicer3 or the command-line EMSegment executable.
 == Usage ==
 ===Examples, Use Cases & Tutorials===
@@ Line 37: / Line 51: @@
 ===Quick Tour of Features and Use===
-List all the panels in your interface, their features, what they mean, and how to use them. For instance:
+====Steps in the Workflow Wizard====
-* '''Input panel:'''
+The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides.]]
-== Development ==
+The module is implemented as a programmatic Slicer3 module because it
 ===Dependencies===
-Other modules or packages that are required for this module's use.
+Slicer3 base modules.
 ===Known bugs===
@@ Line 57: / Line 86: @@
 ===Usability issues===
 Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.
 ===Source code & documentation===
-Customize following [http://viewvc.slicer.org/viewcvs.cgi/ links] for your module.
+[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ Links] for the module.
+*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]
-[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.
+*API: [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentMRMLManager.html MRML Manager] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentLogic.html Module Logic] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentGUI.html Module GUI]
 == More Information ==
+For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]
 ===Acknowledgment===
-Include funding and other support here.
+Funding for the EMSegmenter module was provided by NAMIC.
 ===References===
-Publications related to this module go here. Links to pdfs would be useful.
+Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212.

@@ Line 13: / Line 13: @@
 ===Module Type & Category===
-Type: Interactive or CLI
+Type: Interactive
-Category: Base or (Filtering, Registration, ''etc.'')
+Category: Segmentation
 ===Authors, Collaborators & Contact===
-* Author1: Affiliation & logo, if desired
+* Kilian Pohl: Harvard/BWH
-* Contributor1: Affiliation & logo, if desired
+* Brad Davis: Kitware, Inc.
-* Contributor2: Affiliation & logo, if desired
+* Sebastien Barre: Kitware, Inc.
-* Contact: name, email
+* Yumin Yuan: Kitware, Inc.
 ===Module Description===
-Overview of what the module does goes here.
+The EMSegment template builder module is the primary Slicer3 interface to the EMSegment algorithm.  The target audience for this module is someone familiar with brain atlases and tissue labels, not a computer scientist.  It allows the user to configure the algorithm---step-by-step---to a variety of imaging protocols and anatomical structures, and then apply the algorithm to segment data.  Configuration settings are stored in an EMSegment parameters node in the Slicer3 MRML tree.  These settings can be saved and later applied to new data via any of the EMSegment interfaces within Slicer3 or the command-line EMSegment executable.
 == Usage ==