Full-body Shell Creation For CAD Virtual Human S Including .

Full-body Shell Creation for CAD Virtual Humans includingTightly-Spaced, Enclosed ShellsbyAung Thu HtetA ThesisSubmitted to the Facultyof theWORCESTER POLYTECHNIC INSTITUTEin partial fulfillment of the requirements for theMaster of ScienceInElectrical and Computer EngineeringDecember 2017APPROVED:Prof. Sergey MakarovWorcester Polytechnic InstituteDr. Gregory NoetscherUS Army Natick Soldier Research, Development, and Engineering CenterDr. Louis ChenBose CorporationDr. Janakinadh YanamadalaMathWorks, Inc.

iiTo my family and friendsii

iiiAbstractComputational human models have become essential in several different biomedical andelectrical engineering research areas. They enable scientists to study, model, and solvecomplex problems of human body responses to various external stimuli includingelectromagnetic and radio-frequency signals.This study describes the algorithms and procedures of creating multi-tissue full-bodyComputer-Aided Design (CAD) human models. An emphasis is made on full-body shellsof variable thicknesses, e.g. skin, fat, and average body container shells. Such shells,along with internal organs, are useful for multiple high- and low-frequency simulations ina variety of applications.Along with the creation of full-body models, an automatic algorithm to selectivelydecimate the meshes based on average surface curvature is developed. The algorithm willsignificantly reduce model size while keeping the same interpolation accuracy.I defend:1. Creation of Tightly-Spaced Enclosed Full-body Shells of CAD Human MaleModel Using software tools ITK-snap, MeshLab, and MATLAB2. Creation of Full-body CAD Human Female Model with Ear Canals of VariableThicknesses3. Development of Selective Decimation Algorithm based on Average SurfaceCurvature in MATLABiii

ivAcknowledgementMany thanks to Professor Sergey Makarov for his continuous guidance throughout thiswork. His vast knowledge, valuable advice, and dedication have been crucial to thesuccessful outcome of this study.I would also like to sincerely thank Dr. Gregory Noetscher of US Army Natick SoldierResearch, Development, and Engineering Center. I am grateful for his critical advice onseveral major elements of this work, especially development of selective decimationalgorithm based on surface curvature.I would also like to thank fellow students I have worked with during this study Janakinadh Yanamadala, Anh Le Tran, Harshal Tankaria, Edward Burnham, NicholasMaino, and Patrick Lacroix. I had a chance to learn much from them includingMATLAB, SpaceClaim, among various other tools and methodologies.iv

vTable of ContentsHaveFull-body Shell Creation for CAD Virtual Humans including. iTightly-Spaced, Enclosed Shells . iAbstract . iiiAcknowledgement . ivTable of Contents . vList of Figures . viiiList of Tables . xiList of Published and Accepted Papers . xiiCHAPTER 1 . 1OVERVIEW OF FULL-BODY COMPUTATIONAL CAD MODELS . 11.1.Introduction. 11.2.Overview of Full-Body Human Models . 1References . 6CHAPTER 2 . 8METHODS OF CAD MODEL CREATION . 82.1Introduction. 82.2Segmentation . 82.2.1. Manual Segmentation [1] . 92.2.2 Semi-Automatic Segmentation [1] . 102.2.3 Automatic Segmentation . 102.2.4. SimNIBS[16] . 122.2.4.1. Electric Field Calculation Using SimNIBS . 122.2.4.2. Importing SimNIBS Simulation Data into MATLAB . 152.2.4.3. Importing Coil Model Into MATLAB . 182.3Decimation . 192.4Mesh Processing . 20v

vi2.4.1. Triangle Quality and Mesh Quality [10] . 202.4.2. Smoothing. 212.5Validation of Models . 222.6.1. Specific Conditions for CAD Models [10] . 22References . 24CHAPTER 3 . 26DECIMATION BASED ON SURFACE CURVATURE . 263.1Introduction. 263.1.13.2Mesh Decimation [1] . 26Calculation of Surface Curvature . 273.2.1Calculation of Normal Vectors . 283.2.2Determining Neighboring Triangles . 283.2.2.1Arrays of Vertices and Faces [1] . 293.2.2.1 Determining Neighboring Triangles . 313.2.2.2. Calculation of Angle between Normal Vectors . 323.3Decimation on Area of Lower Curvature . 333.4Local Laplacian Smoothing . 363.4.1Necessity of Mesh Smoothing [1] . 363.4.2Topology-preserving Laplacian smoothing [1]. 37Laplacian Smoothing with Re-triangulation. Iterative Algorithm [1] . 393.4.3Weaknesses of Laplacian Smoothing[1] . 403.4.4Local . 41References . 43CHAPTER 4 . 44METHODS OF FULL-BODY SHELL CREATION . 444.1Introduction. 444.2Skin Shell . 454.3Fat Shell . 464.4Average Body Shell . 474.5Skin, Fat, and Average Body Shells . 48vi

viiReferences . 49CHAPTER 5 . 51FULL-BODY SHELLS FOR VHP-MALE CAD MODEL . 515.1Introduction. 515.2Mesh Healing in ANSYS SpaceClaim . 515.2.1Resolving Non-manifoldness and Holes . 515.2.2Resolving Self-Intersections in Individual Shells . 545.2.3Resolving Intersections among Shells . 565.2.4Resolving Issue of Multiple Pieces . 595.3Separating Arms from Torso . 605.4Final Shells . 62CHAPTER 6 . 64FULL-BODY SHELLS FOR VHP-FEMALE CAD MODEL WITH EAR CANAL . 646.1 Introduction . 646.2 Segmentation of the Ear Canals . 656.4Variable Thicknesses in Female Head with Ear Canals . 67. 686.4.1Extraction of Ears . 696.4.2Removal of Ears . 706.4.3Integrating Extracted Ears into Shell with Removed Ears . 706.4.4Healing Meshes . 716.4.5Final Shells with Variable Thicknesses . 72CHAPTER 7 . 75DISCUSSION AND CONCLUSIONS . 75Appendix A: Decimation Based on Surface Curvature . 76Appendix B: Segmentation Result of VHP-Female Intestine . 79vii

viiiList of FiguresFigure 1: Members of Virtual Population [4]-[6] . 4Figure 2: Full-body Male Model from Zygote Media Group, Inc. [7][7] . 4Figure 3: VHP-Female v. 3.0 CAD model [8]-[13] with about 250 individual parts; sometissues have been removed for visual clarity.[2] . 5Figure 4: Image of a patella with a traced boundary; b) – resulting point cloud; c) –patella CAD model; d) – patella voxel model.[1] . 9Figure 5: FreeSurfer Segmentation of White Matter[13]. 11Figure 6: FreeSurfer FreeView Visualization Tool . 11Figure 7: Example Mesh Loaded in SimNIBS GUI. Original Drawing using SimNIBSGUI . 13Figure 8: Adding TMS Position and Direction Reference to SimNIBS Model. OriginalDrawing using SimNIBS GUI . 13Figure 9: Adding Coil Definition File to SimNIBS. Original Drawing using SimNIBSGUI . 14Figure 10: SimNIBS Simulation Result Viewed using Gmsh. Original Drawing usingGmsh Tool . 15Figure 11: Saving STL File of Mesh in Gmsh. Original Drawing using Gmsh Tool . 16Figure 12: Electric Field Data Imported as Matrix in MATLAB . 17Figure 13: Electric Field Data Plotted in MATLAB. Original Drawing using SimNIBSExample Head Model . 17Figure 14: SimNIBS Coil Model Visualized in MATLAB. Original Drawing usingSimNIBS Coil. . 18Figure 15: Original Mesh and Decimated Mesh. Original drawing . 19Figure 16: Radii of the inscribed circle (largest circle contained in the triangle) and thecircumscribed circle (smallest circle containing the triangle), respectively, for a rightangled isosceles triangle. rin is called the inradius and rout is the circumradius. . 21Figure 17: Mesh Smoothing. Original drawing . 22Figure 18:. a) – Examples of a manifold edge; b) – non-manifold edge, and c) – nonmanifold node. [10]. 22Figure 19: Three types of intersection of a triangle from a master mesh X with varioustriangles of a slave mesh Y. Cases #1 and #3 are equivalent if we treat the master andslave meshes as one set of triangles. Original Drawing from R.[10]. 23Figure 20: a) - Edge collapse method; b) – vertex removal. Original Drawing fromRef.[1] . 27Figure 21: Surface Curvature at a Triangle Depicting Neighboring Triangles and theNormal Vectors. Original Drawing using Mesh Loaded in Meshlab . 28viii

ixFigure 22: Normal of a Triangle. Drawing taken e.html) . 28Figure 23: Mesh generation for a planar rectangle. Drawing from Ref. [1]. . 29Figure 24: Demonstration of Curvature Calculation. Original Drawing using cylindermesh taken from nge/32573-patchcurvature) . 33Figure 25: Decimation Result of Algorithm (5 iterations). Original Drawing . 35Figure 26: Decimation Result of Algorithm (25 iterations). Original Drawing . 35Figure 27: Problem geometry with non-intersecting boundaries and the initial meshes.Drawing from Ref.[1] . 37Figure 28: Concept of Laplacian smoothing. Drawing from Ref. [1]. 38Figure 29: Results of Laplacian smoothing with algorithm WCC after 9th iteration.Drawing from Ref. [1] . 40Figure 30: Decimation of Lower Curvature Area (25 iterations) with Local LaplacianSmoothing on Attached Nodes of Deleted Vertex. Original Drawing . 41Figure 31: Decimation of Lower Curvature Area (25 iterations) with Local LaplacianSmoothing on More Nodes. Original Drawing . 42Figure 32: Local mesh shrinkage and/or expansion according to Eq. (4.1). Drawing fromRef [17] . 45Figure 33: VHP-Female Skin Shell. Original Drawing . 45Figure 34: Skin Shell and Fat Shell with 1mm thickness. Original Drawing . 46Figure 35: Fat Shell and Average Body Shell with 2mm thickness. Original Drawing . 47Figure 36: Skin Shell, Fat Shell and Average Body Shell. Original Drawing . 48Figure 37: SpaceClaim Check Mesh. Original Drawing in SpaceClaim . 52Figure 38: Non-Manifoldness Detection in SpaceClaim. Original Drawing in SpaceClaim. 52Figure 39: Marked Non-Manifold Triangle Zoomed In. Original Drawing in SpaceClaim. 53Figure 40: Non-Manifold Triangles Identified. Original Drawing in SpaceClaim . 53Figure 41: Non-Manifold Triangles Removed. Original Drawing in SpaceClaim . 54Figure 42: Intersections detected in SpaceClaim. Original Drawing in SpaceClaim . 54Figure 43: Intersections in Fingers and Groin Areas. Original Drawing in SpaceClaim . 55Figure 44: Intersections in Toes. Original Drawing in SpaceClaim . 55Figure 45: Resolving Intersections by Moving the Triangles. Original Drawing inSpaceClaim . 56Figure 46: Resolving Intersections by Reconstruction. Original Drawing in SpaceClaim. 56Figure 47: Visualization of Intersections between Two Shells. Original Drawing inSpaceClaim . 57ix

xFigure 48: Resolving Intersections between Two Shells. Original Drawing in SpaceClaim. 58Figure 49: SpaceClaim Tools for Joining and Separating Two Shells. Original Drawing inSpaceClaim

Original Drawing in SpaceClaim . 53 Figure 41: Non-Manifold Triangles Removed. Original Drawing in SpaceClaim . 54 Figure 42: Intersections detected in SpaceClaim. Original Drawing in SpaceClaim . 54 Figure 43: Intersections in Fingers and Groin Areas. Original Drawing in S