Difference between revisions of "Modules:GyriContourSegmentation-Documentation-3.5"

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[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
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[[Documentation-3.6|Return to Slicer 3.5 Documentation]]
 
__NOTOC__
 
__NOTOC__
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===Gyri Contour Segmentation===
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===Mesh Contour Segmentation===
 
MyModule
 
MyModule
  
 
{|
 
{|
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|[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
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|[[Image:brainH.png|thumb|280px|Surface Normal Curvature]]
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|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
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|[[Image:tumor2_init_4.PNG|thumb|280px|Initial Points From User]]
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|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]
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|[[Image:tumor_conv_3.png|thumb|280px|Converged Contour on Surface]]
 
|}
 
|}
  
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===Module Description===
 
===Module Description===
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This module proves the Riemann zeta-hypothesis
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This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).
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 +
The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.
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While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).
  
 
== Usage ==
 
== Usage ==
  
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===Examples, Use Cases & Tutorials===
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===Use Cases, Examples===
  
 
* Note use cases for which this module is especially appropriate, and/or link to examples.
 
* 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 examples of the module's use
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* Link to any existing tutorials
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===Tutorials===
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* Tutorial 1
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* Data Set 1
  
 
===Quick Tour of Features and Use===
 
===Quick Tour of Features and Use===
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List all the panels in your interface, their features, what they mean, and how to use them. For instance:
 
  
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A list panels in the interface, their features, what they mean, and how to use them. For instance:
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 +
{|
 +
|
 
* '''Input panel:'''
 
* '''Input panel:'''
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** '''First input'''
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** '''Second input'''
 
* '''Parameters panel:'''
 
* '''Parameters panel:'''
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** '''First parameter'''
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** '''Second parameter'''
 
* '''Output panel:'''
 
* '''Output panel:'''
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** '''First output'''
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** '''Second output'''
 
* '''Viewing panel:'''
 
* '''Viewing panel:'''
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|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
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|}
  
 
== Development ==
 
== Development ==
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 +
===Notes from the Developer(s)===
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 +
Algorithms used, library classes depended upon, use cases, etc.
  
 
===Dependencies===
 
===Dependencies===
  
 
Other modules or packages that are required for this module's use.
 
Other modules or packages that are required for this module's use.
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 +
===Tests===
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On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:
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* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
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* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]
  
 
===Known bugs===
 
===Known bugs===
  
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Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.
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Links to known bugs in the Slicer3 bug tracker
  
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* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]
  
  
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===Source code & documentation===
 
===Source code & documentation===
  
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Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.
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Links to the module's source code:
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[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.
 
  
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Source code:
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*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
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*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]
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Doxygen documentation:
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*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]
  
 
== More Information ==  
 
== More Information ==  
  
 
===Acknowledgment===
 
===Acknowledgment===
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Include funding and other support here.
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This  work  was  supported  in  part  by  grants  from  NSF, AFOSR, ARO, as well as by a grant from
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NIH (NAC P41 RR-13218) through Brigham and Women’s
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Hospital. An NSF Fellowship supported part of the work.
  
 
===References===
 
===References===
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Publications related to this module go here. Links to pdfs would be useful.
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 +
P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.
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[[File:pkmesh-spie.pdf]]

Latest revision as of 20:19, 10 June 2010

Home < Modules:GyriContourSegmentation-Documentation-3.5

Return to Slicer 3.5 Documentation

Mesh Contour Segmentation

MyModule

Surface Normal Curvature
Initial Points From User
Converged Contour on Surface

General Information

Module Type & Category

Type: CLI

Category: Segmentation

Authors, Collaborators & Contact

  • Peter Karasev (Author): Georgia Tech
  • Allen Tannenbaum (Collaborator): Georgia Tech
  • Ron Kikinis (Collaborator): Harvard Medical School SPL
  • Jimi Macolm (Collaborator): Harvard Medical School SPL / Georgia Tech
  • Contact: Peter Karasev, pkarasev@gatech.edu

Module Description

This module is a tool to generate closed contours on a surface in 3D. The contour is initialized with a set of points, and subsequently 'evolves' according to some geometric criterion of the underlying surface (e.g. Surface Normal, mean curvature, second fundamental form, etc) and the embedded curve (e.g. geodesic & normal curvatures, etc ).

The implementation uses a version of Sparse Field Level Sets (Whitaker et al 1998) modified for a mesh where there is an arbitrary number of vertex neighbors.

While the motivating problem is segmentation of Sulci & Gyri on the cortical surface, the technique is also applicable to analysis of other anatomic structures (e.g. bones and fractures thereof).

Usage

Use Cases, Examples

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

Tutorials

  • Tutorial 1
  • Data Set 1

Quick Tour of Features and Use

A list panels in the interface, their features, what they mean, and how to use them. For instance:

  • Input panel:
    • First input
    • Second input
  • Parameters panel:
    • First parameter
    • Second parameter
  • Output panel:
    • First output
    • Second output
  • Viewing panel:
User Interface

Development

Notes from the Developer(s)

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

Dependencies

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

Tests

On the Dashboard, these tests verify that the module is working on various platforms:

Known bugs

Links to known bugs in the Slicer3 bug tracker


Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.

Source code & documentation

Links to the module's source code:

Source code:

Doxygen documentation:

More Information

Acknowledgment

This work was supported in part by grants from NSF, AFOSR, ARO, as well as by a grant from NIH (NAC P41 RR-13218) through Brigham and Women’s Hospital. An NSF Fellowship supported part of the work.

References

P.A. Karasev, J.G. Malcolm, M. Niethammer, R. Kikinis, A. Tannenbaum. User-Driven 3D Mesh Region Targeting. To appear in SPIE Medical Imaging 2010.

Pkmesh-spie.pdf

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