Oct 30, 2005 Sylvain Jaume 1

Open Topology:A Toolkit for Brain

Isosurface Correction

Sylvain JAUME(1), Patrice RONDAO(2), Benoit MACQ(2)

(1) Kitware Inc., (2) University of Louvain

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Visualization of the Brain

Speech, vision, etc. lie in the outer layer.

surface visualization

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Visualization of the Brain3D Image

Segmentation

Marching Cubes

Smoothing

Mesh

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Visualization of the Brain3D Image

Segmentation

Marching Cubes

Smoothing

Mesh

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Visualization of the Brain3D Image

Segmentation

Marching Cubes

Smoothing

Mesh

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Visualization of the Brain3D Image

Segmentation

Marching Cubes

Smoothing

Mesh with Handles

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Visualization of the Brain3D Image

Segmentation

Marching Cubes

Smoothing

Mesh with Handles

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Visualization of the Brain3D Image

Segmentation

Marching Cubes

Smoothing

Mesh with Handles

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Visualization of the Brain3D Image

Segmentation

Marching Cubes

Smoothing

Mesh with Handles

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Visualization of the Brain3D Image

Segmentation

Marching Cubes

Smoothing

Mesh with Handles

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Visualization of the Brain

• Where do handles come from ?

Limited resolution

Scanner artifacts

Segmentation errors

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Visualization of the Brain

• Does it really matter ???

For 3D visualization

For distance measurements

For EEG source localization

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State of the Art

• Image methods– Malandain 93, Shattuck 01, Kriegeskorte 01

• Mesh methods– Fischl 01, Guskov 01, Wood 04, Segonne 05

• Graph methods– Han 02, Segonne 03

• Level-Set methods– Han 01, Bischoff 02

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Contributions

No region is left out

Fast (less than 2 min)

Open Source

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Algorithm Overview

Marching Cubes

Handle Detection

Handle Correction

3D Image Triangle Mesh

Corrected 3D Image

Contours

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Algorithm Overview

Marching Cubes

Handle Detection

Handle Correction

3D Image Triangle Mesh

Contours

Corrected 3D Image

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Algorithm Overview

Marching Cubes

Handle Detection

Handle Correction

3D Image Triangle Mesh

Contours

Corrected 3D Image

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Algorithm Overview

Marching Cubes

Handle Detection

Handle Correction

3D Image Triangle Mesh

Polylines

Corrected 3D Image

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Algorithm Overview

Marching Cubes

Handle Detection

Handle Correction

3D Image Triangle Mesh

Contours

Corrected 3D Image

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Algorithm Overview

Marching Cubes

Handle Detection

Handle Correction

3D Image Triangle Mesh

Contours

Corrected 3D Image

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Algorithm Overview

Marching Cubes

Handle Detection

Handle Correction

3D Image Triangle Mesh

Contours

Corrected 3D Image

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Algorithm Overview

Marching Cubes

Handle Detection

Handle Correction

3D Image Triangle Mesh

Contours

Marching Cubes Corrected Mesh

Corrected 3D Image

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Algorithm Overview

Marching Cubes

Handle Detection

Handle Correction

3D Image Triangle Mesh

Contours

Marching Cubes Corrected Mesh

Corrected 3D Image

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Key Points

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1. Embracing the Handle

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1. Embracing the Handle

• Init

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1. Embracing the Handle

• Init

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1. Embracing the Handle

• Init

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1. Embracing the Handle

• Init

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1. Embracing the Handle

• Split

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1. Embracing the Handle

• Split

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1. Embracing the Handle

• Split

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1. Embracing the Handle

• Merge

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1. Embracing the Handle

• Merge

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1. Embracing the Handle

• Merge

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1. Embracing the Handle

• Merge

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1. Embracing the Handle

• Merge

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1. Embracing the Handle

• Merge

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1. Embracing the Handle

• Finalize

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1. Embracing the Handle

• Finalize

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1. Embracing the Handle

• Finalize

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2. Holding it Tight

• Distance

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2. Holding it Tight

• Distance

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2. Holding it Tight

• Distance

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2. Holding it Tight

• Distance

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2. Holding it Tight

• Distance

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2. Holding it Tight

• Distance

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2. Holding it Tight

• Distance

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2. Holding it Tight

• Distance

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2. Holding it Tight

• Distance

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3. Filling the Handle

• New pixel intensity inside the loop

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Putting it Together

1. Handle Detection– Embracing the handle

2. Handle Localization– Holding it tight

3. Handle Correction– Filling the handle

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Performance

• g: genus, i.e. number of handles• V: number of vertices• E: number of edges• F: number of faces• C: number of connected components

Euler Characteristic

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Data Structures

vtkCellLinks

vtkPoints vtkCellArray

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Data Structures

• Edge to Start Point• Edge to End Point

• Edge to Polygon

vtkPoints vtkCellArray Half-Edge

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Data Structures

• Edge to Reverse Edge• Edge to Parent Edge

vtkPoints vtkCellArray Half-Edge

Detection

Localization

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Data Structures

• Edge to Contour• Edge to Distance

vtkPoints vtkCellArray Half-Edge

Detection

Localization

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Data Structures

Extended Half-Edge Structure:• Edge to Polygon• Edge to Start Point• Edge to End Point• Edge to Reverse Edge• Edge to Parent Edge• Edge to Contour• Edge to Distance

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Code

• vtkHandleDetection– Half-edge structure– Area growing– Shortest loop

• vtkHandleCorrection– Loop to image– Water-tight region

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Goal

Correct EVERY handle FAST!

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Perspectives

Visualization, measurements, source localization

Benchmarking with other methods

Half-Edge algorithms

Integration into CARET Software

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MICCAI Open Source Workshop

• "Open Topology: A Toolkit for Brain Isosurface Correction", Jaume, Rondao, Macq, MICCAI WS 2005.

• Article• Code• Data• Demo

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www.OpenTopology.org

• Algorithm

• Source code

• Documentation

• Data

• Updates