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:

• MyModuleTest1 MyModuleTest1.cxx
• MyModuleTest2 MyModuleTest2.cxx

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:

• file.cxx
• file.h

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.