Modules:MeshContourSegmentation-Documentation-3.6
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Mesh Contour Segmentation
MyModule
General Information
Module Type & Category
Type: CLI
Category: Segmentation
Authors, Collaborators & Contact
- Peter Karasev (Author): Georgia Tech
- Karol Chudy (Author): Georgia Tech
- Allen Tannenbaum (Collaborator): 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
1. Compute & Display surface mean curvature, when noise in the mesh precludes the ITK function of similar purpose from producing good result:
2. Mark and Display segment of the surface in virtual colonoscopy, e.g. to mark a tumor location
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:
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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:
-Only VTK & STL
Tests
On the Dashboard, these tests verify that the module is working on various platforms:
http://www.cdash.org/CDash/testDetails.php?test=52059394&build=600130
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:
Several Key Points:
- Entry Point from Slicer
- Computation of Initial Path from Un-Ordered Initial Points
- Adjacency Tree, Mean Curvature, Curvature Surface Gradient Computation
- Levelset Evolution Entry Point
- Levelset Evolution Core
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.
