The VHP-F Computational Phantom and its Applications for Electromagnetic Simulations by Gregory Michael Noetscher A Dissertation Submitted to the Faculty of the WORCESTER POLYTECHNIC INSTITUTE in partial fulfillment of the requirements for the Degree of Doctor of Philosophy in Electrical and Computer Engineering April 2014 APPROVED: Dr. Sergey Makarov ___________________________________ Worcester Polytechnic Institute Dr. Mikhail Kozlov ___________________________________ Max Planck Institute for Human Cognitive and Brain Sciences Dr. Andrew Cavanaugh ____________________________________ Naval Undersea Warfare Center Dr. Vishwanath Iyer ____________________________________ The Mathworks, Inc. Dr. Ara Nazarian ____________________________________ Beth Israel Deaconess Medical Center To Nelson Hettler, P.E. for providing the spark that has turned into a lifelong pursuit of engineering. ii Abstract Modeling of the electromagnetic, structural, thermal, or acoustic response of the human body to various external and internal stimuli is limited by the availability of anatomically accurate and numerically efficient computational models. The models currently approved for use are generally of proprietary or fixed format, preventing new model construction or customization. 1. This dissertation develops a new Visible Human Project – Female (VHP-F) computational phantom, constructed via segmentation of anatomical cryosection images taken in the axial plane of the human body. Its unique property is superior resolution on human head. In its current form, the VHP-F model contains 33 separate objects describing a variety of human tissues within the head and torso. Each obejct is a non-intersecting 2-manifold model composed of contiguous surface triangular elements making the VHP-F model compatible with major commercial and academic numerical simulators employing the Finite Element Method (FEM), Boundary Element Method (BEM), Finite Volume Method (FVM), and Finite-Difference Time- Domain (FDTD) Method. 2. This dissertation develops a new workflow used to construct the VHP-F model that may be utilized to build accessible custom models from any medical image data source. The workflow is customizable and flexible, enabling the creation of standard and parametrically varying models facilitating research on impacts associated with fluctuation of body characteristics (for example, skin thickness) and dynamic processes such as fluid pulsation. 3. This dissertation identifies, enables, and quantifies three new specific computational bioelectromagnetic problems, each of which is solved with the help of the developed VHP-F model: I. Transcranial Direct Current Stimulation (tDCS) of human brain motor cortex with extracephalic versus cephalic electrodes; II. RF channel characterization within cerebral cortex with novel small on-body directional antennas; III. Body Area Network (BAN) characterization and RF localization within the human body using the FDTD method and small antenna models with coincident phase centers. Each of those problems has been (or will be) the subject of a separate dedicated MS thesis. iii Acknowledgement While this dissertation represents the culmination of my time as a PhD candidate in the Electrical and Computer Engineering Department at Worcester Polytechnic Institute, the research goals described herein were not accomplished in isolation and I wish to thank the many individuals that contributed along the way. First and foremost, I would like to thank Prof. Sergey Makarov for advising this work and providing incredible leadership and guidance during these past five years. His commitment to his students and his motivation are truly inspirational; he has provided an example to which I shall strive to achieve for the remainder of my career. I wish to thank Dr. Alvaro Pascual-Leone, Prof. Reinhold Ludwig, Prof. Peder Pedersen, and Dr. Francesca Scire-Scappuzzo for providing exceptional direction that has significantly shaped the outcome of this work. Thank you also to Dr. Mikhail Kozlov of the Max Planck Institute for Human Cognitive and Brain Sciences, Dr. Ara Nazarian of Beth Israel Deaconess Medical Center, Dr. Andrew Cavanaugh of the Naval Undersea Warfare Center and Dr. Vishwanath Iyer of The Mathworks – I am supremely humbled to have committee members of such high esteem. Thank you to Dr. Alexander Prokop and Dr. Tilmann Wittig of Computer Simulation Technology and Dr. Sara Louie of ANSYS, Inc. for providing compatibility and performance analysis of the VHP-F computational phantom. Their insight regarding the integration of the model into their respective softwares and the typical desires of potential customers using human body models for electromagnetic analysis has been very important in the development of the model. Thank you to the students that I have interacted with at WPI, including Jeffrey Elloian, Janakinadh Yanamadala, Aung Thu Htet, Saili Maliye, David Quinn and Chas Frick. Best of luck to all of you all! I would also like to thank my mom, Cheryl Noetscher, for lifelong support in pursuing my goals and for demonstrating that it is possible to simultaneously raise a family, have a successful career and achieve academic excellence. iv Finally, I wish to thank my wife Yen, who has made innumerable sacrifices in order for me to complete this work. A very special thank you is reserved for our children, Jennifer and Benjamin - your openness and willing attitude toward learning have been a motivating force that drives me. May you carry this on throughout your lives! v Table of Contents Abstract .......................................................................................................................................... iii Acknowledgement ......................................................................................................................... iv Table of Contents ........................................................................................................................... vi List of Figures ............................................................................................................................... xii List of Tables .............................................................................................................................. xvii List of Published and Accepted Papers ...................................................................................... xviii Chapter 1 – Introduction ................................................................................................................. 1 1.1 Existing commercial models ............................................................................................ 3 1.2 Existing commercial workflow and segmentation tools .................................................. 5 1.3 Existing open-source segmentation tools ......................................................................... 5 1.4 Dissertation organization ...................................................................................................... 6 References ................................................................................................................................... 6 Chapter 2 – Theory of triangular surface meshes ......................................................................... 11 2.1 Triangular mesh and its quality ...................................................................................... 12 2.1.1 Triangular mesh type ................................................................................................... 13 2.1.2 Triangular mesh quality ............................................................................................... 14 2.2 Delaunay triangulation ........................................................................................................ 16 2.2.1 Delaunay Triangulation Algorithm .............................................................................. 17 2.2.2 Constrained Delaunay Triangulation ........................................................................... 18 2.3 Mesh Transformations ........................................................................................................ 19 2.4 Mesh generation and improvement ..................................................................................... 20 2.4.1 Laplacian Smoothing ................................................................................................... 20 2.4.2 Mesh Decimation ......................................................................................................... 23 2.5 Adaptive mesh refinement and mesh gradation .................................................................. 24 2.6 Implicit boundary description ............................................................................................. 31 2.6.1 Mesh size function ....................................................................................................... 32 2.7 Creating 2-manifold surface meshes ................................................................................... 33 vi 2.8 A Note on Constructive Solid Geometry ............................................................................ 34 References ................................................................................................................................. 40 Chapter 3 – Image segmentation................................................................................................... 44 3.1 Basic principles of image segmentation ............................................................................