Modules:MeshContourSegmentation-Documentation-3.6

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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
• 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:

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:

-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

• Bug 000: description

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:

• All 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:

• class1

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.