Lecture 20
Transcript of Lecture 20
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Surface Modeling Visualization using BrainVISA
Bill RogersUTHSCSA – Research Imaging Center
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Why Use Surface Modeling
• Visualization of Structure• Analysis of Structure• Dynamic control of view
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What Makes a Surface
• A surface is usually defined as a mesh• The mesh is composed of vertices, edges,
normals and polygons• The vertices define the surface boundary• Vertices are connected by edges• Edges are combined to make polygons• Normals determine side of surface as well as
viewing properties
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Vertices and Edges
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Polygons
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Polygon Mesh Surface
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Parametric Surfaces
• Surface in Euclidean space defined by a parametric equation with two parameters
• A set of weighted control points determine the location of individual surface points
• The come in several flavors including Bezier, B-Spline, NURBS
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NURBS surface with control points
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NURBS Surfaces
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Isosurface extractionor
Where to put the surface
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Isosurfaces
• A 3-D surface corresponding to points with a single scalar value (or narrow range of values).
• The scalar value corresponds to an interface between voxels of different properties.
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The Surface is Only as Good as the Tissue Classification
• Bias Correction• Partial Volume Effect• Classification of voxels
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Isosurface Extraction Techniques
• Geometric Decomposition Techniques– Geometric techniques retain the original
representation of the volume and partition along divisions in the voxel volume
• Span Space Decomposition Techniques– Span space decomposition techniques create and
manipulate abstract representations of the voxels
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Methods of Isosurface Extraction
• Marching Cubes (Geometric)
• BONO - branch-on-need octree (Geometric)
• ISSUE - Isosurfacing in Span Space with Utmost Efficiency (Span Space)
• Interval Tree – (Span Space)
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Marching Cubes
• William E. Lorensen, Harvey E. Cline: Marching Cubes: A high resolution 3D surface construction algorithm. In: Computer Graphics, Vol. 21, Nr. 4, July 1987
• Computes polygons where the isosurface passes through eight nearest neighbors
• Gradient of scalar value at each grid point used for surface normal
• Other algorithms are always compared to Marching Cubes
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Marching Cubes• 15 Unique cube configurations that can be
rotated and reflected to 256 configurations
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Marching Cubes DemoGraphics cards aren’t just for games anymore
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Mesh Segmentation
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Introduction to BrainVisa• Origin and Development
• Collaborative work of methodologists of the Institut Fédératif de Recherche
• Core development now at the Service Hospitalier Frédéric Joliot
• Framework for Image Processing• GUI for chaining applications together
– GUI developed in Python– Command line application developed in C++
• Database for organization of input and output files• Visualization package for viewing results
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BrainVISA Availability
• Multiplatform– Linux (Fedora, Redhat, Mandriva)– Macintosh (OS X)– Windows (2000, XP)
• Download at http://brainvisa.info/
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BrainVISA Demo
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BrainVISA Curvature Mapping
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BrainVISA Cortical Folds
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RIC BrainVisa Extensions
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RIC Cortical Thickness
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White matter surface normals
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RIC Sulcal Length and Depth
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Mapping Mesh to Volume
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RIC 3D Gyrification Index
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Removing Effect of Ventricles