Modules:LesionSegmentationApplications-Documentation-3.6 - Revision history

Mscully: /* Authors, Collaborators & Contact */ Updated email addr.

2011-11-10T19:24:39Z

Authors, Collaborators & Contact: Updated email addr.

Kikinis: /* Module Description */

2010-05-21T13:31:43Z

Module Description

Mscully: /* References */ Added segmentation method paper

2010-04-10T16:25:31Z

References: Added segmentation method paper

Mscully: /* Quick Tour of Features and Use */

2010-04-07T02:40:20Z

Quick Tour of Features and Use

Mscully: /* Lupus Lesion Segmentation Applications */

2010-04-07T01:50:04Z

Lupus Lesion Segmentation Applications

Mscully: /* Lupus Lesion Segmentation Applications */

2010-04-06T22:31:31Z

Lupus Lesion Segmentation Applications

Mscully: Intital page

2010-04-06T22:27:45Z

Intital page

New page

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Lupus Lesion Segmentation Applications===

{|
|[[File:LesionFlowChart.jpg|thumb|200px|Lesion Segmentation Method Overview]]
|}

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

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Author1: Mark Scully, The Mind Research Network
* Author2: H. J. Bockholt, The Mind Research Network
* Contributor1:
* Contact: Mark Scully, mscully[at]mrn[dot]org

===Module Description===
The lupus lesion segmentation applications are a group of tools for segmenting lesions in lupus patients using the T1-weighted, T2-weighted, and FLAIR images. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line.

== Usage ==

===Use Cases, Examples===

This module is specifically for segmenting lesions in lupus patients.
===Tutorials===

* Tutorials:
** [[Media:Slicer3Training_WhiteMatterLesions_v2.3.pdf‏| Lesion Segmentation Tutorial PDF]]
* Tutorial Dataset
** [http://www.nitrc.org/frs/download.php/860/LesionSegmentationTutorialData.tgz Download Example dataset]

===Quick Tour of Features and Use===

{|
|
* '''Input:''' set input images representing the different modalities of the same subject
** Input T1 Volume: set input T1-weighted image, if available
** Input T2 Volume: set input T2-weighted image, if available
** Input FLAIR Volume: set input FLAIR image, if available
** Input Brain Mask Volume: set input Brain Mask image, if available
** Lesion segmentation Model File: set to the model file available with the tutorial
** Segmentation atlas type (T1 or T2, default: T1): set segmentation atlas type (should match subject input image)

* '''Output:''' set output image
** Output Lesion Mask Volume: The volume that is the result of the segmentation process

|[[File:Predict_lesion_view.jpg|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

* Slicer3 modules:
**

===Tests===

On the [http://skylla.ia.unc.edu/CDash/index.php?project=ARCTIC Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in 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===

* [https://www.ia.unc.edu/NeuroLib/Release/ARCTIC/ Source code]
* Download release source code via svn:
** cvs -d :pserver:anonymous@www.nitrc.org:/cvsroot/lupuslesion login
** cvs -d :pserver:anonymous@www.nitrc.org:/cvsroot/lupuslesion checkout lupuslesion

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics.

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

← Older revision		Revision as of 16:25, 10 April 2010
Line 96:		Line 96:

	===References===		===References===
−	~~Publications related~~ to ~~this module go here~~. ~~Links to pdfs would be useful~~.	+	Scully M, Anderson B, Lane T, Gasparovic C, Magnotta V, Sibbitt W, Roldan C, Kikinis R and Bockholt HJ (2010) An automated method for segmenting white matter lesions through multi-level morphometric feature classification with application to lupus. Front. Hum. Neurosci. doi:10.3389/fnhum.2010.00027
		+	http://frontiersin.org/neuroscience/humanneuroscience/paper/10.3389/fnhum.2010.00027/

@@ Line 9: / Line 9: @@
 {|
 |[[File:LesionFlowChart.jpg|thumb|200px|Lesion Segmentation Method Overview]]
-|[[File:LesionInBrain.jpg|thumb|200px|Segmented Lesion Volume in Brain]]
+|[[File:LesionsWithVentricles.png|thumb|200px|Segmented Lesion Volume in Brain]]
 |}

@@ Line 20: / Line 20: @@
 ===Authors, Collaborators & Contact===
-* Author1: Mark Scully, The Mind Research Network
+* Author1: Mark Scully, The University of Iowa
 * Author2: H. J. Bockholt, The Mind Research Network
 * Contributor1:
-* Contact: Mark Scully, mscully[at]mrn[dot]org
+* Contact: Mark Scully, mark-scully[at]uiowa[dot]edu
 ===Module Description===

@@ Line 27: / Line 27: @@
 ===Module Description===
 The lupus lesion segmentation applications are a group of tools for segmenting lesions in lupus patients using the T1-weighted, T2-weighted, and FLAIR images. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line.
 == Usage ==

@@ Line 50: / Line 50: @@
 ** Input Brain Mask Volume: set input Brain Mask image, if available
 ** Lesion segmentation Model File: set to the model file available with the tutorial
 * '''Output:''' set output image