Area and Volume Restoration in Elastically Deformable Solids

This paper describes an improvement of a classical energy-based model to simulate elastically deformable solids. The classical model lacks the ability to prevent the collapsing of solids under influence of external forces, such as user interactions and collision. A thorough explanation is given for the origins of instabilities, and extensions that solve the issues are proposed to the physical model. Within the original framework of the classical model a complete restoration of area and volume is introduced. The improved model is suitable for interactive simulation and can recover from volumetric collapsing, in particular upon large deformation

Detection and modelling of contacts in explicit finite-element simulation of soft tissue biomechanics

Realistic modelling of soft-tissue biomechanics and mechanical interactions between tissues is an important part of surgical simulation, and may become a valuable asset in surgical image-guidance. Unfortunately, it is also computationally very demanding. Explicit matrix-free FEM solvers have been shown to be a good choice for fast tissue simulation, however little work has been done on contact algorithms for such FEM solvers. This work introduces such an algorithm that is capable of handling the scenarios typically encountered in image-guidance. The responses are computed with an evolution of the Lagrange-multiplier method first used by Taylor and Flanagan in PRONTO 3D with spatio-temporal smoothing heuristics for improved stability with coarser meshes and larger time steps. For contact search, a bounding-volume hierarchy (BVH) capable of identifying self collisions, and which is optimised for the small time steps by reducing the number of bounding-volume refittings between iterations through identification of geometry areas with mostly rigid motion and negligible deformation, is introduced. Further optimisation is achieved by integrating the self-collision criterion in the BVH creation and updating algorithms. The effectiveness of the algorithm is demonstrated on a number of artificial test cases and meshes derived from medical image data

A virtual environment for the modelling, simulation and manufacturing of orthopaedic devices

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.The objective of this work is to investigate whether the game physics based modelling is accurate enough to be used in modelling the motion of the human body, in particular musculoskeletal motion. Hitherto, the implementation of game physics in the medical field focused only on anatomical representation for education and training purposes. Introducing gaming platforms and physics engines into orthopaedics applications will help to overcome several difficulties encountered in the modelling of articular joints. Implementing a physics engine (PhysX), which is mainly designed for video games, handles intensive computations in optimized ways at an interactive speed. In this study, the capabilities of the physics engine (PhysX) and gaming platform for modelling and simulating articular joints are evaluated. First, a preliminary validation is carried out for mechanical systems with analytical solutions, before constructing the musculoskeletal model to evaluate the consistency of gaming platforms. The developed musculoskeletal model deals with the human joint as an unconstrained system with 6 DOF which is not available with other joint modeller. The model articulation is driven by contact surfaces and the stiffness of surrounding tissues. A number of contributions, such as contact modelling and muscle wrapping, have been made in this research to overcome some existing challenges in joint modelling. Using muscle segmentation, the proposed technique effectively handles the problem of muscle wrapping, a major concern for many; thus the shortest path and line of action are no longer problematic. Collision behaviour has also shown a stable response for colliding as well as resting objects, provided that it is based on the principles of surface properties and the conservation of linear and angular momentums. The precision of collision detection and response are within an acceptable tolerance controllable by varying the mesh density. An image based analysis system is developed in this thesis, mainly in order to validate the proposed physics based modelling solution. This minimally invasive method is based on the analysis of marker positions located at bony positions with minimal skin movement. The image based system overcomes several challenges associated with the currently existing methods, such as inaccuracy, complication, impracticability and cost. The analysis part of this research has considered the elbow joint as a case study to investigate and validate the proposed physics based model. Beside the interactive 3D simulation, the obtained results are validated by comparing them with the image based system developed within the current research to investigate joint kinematics and laxity and also with published material, MJM and results from experiments performed at the Brunel Orthopaedic Research and Learning Centre. The proposed modelling shows the advantageous speed, reliability and flexibility of the proposed model. It is shown that the gaming platform and physics engine provide a viable solution to human musculoskeletal modelling. Finally, this thesis considers an extended implementation of the proposed platform for testing and assessing the design of custom-made implants, to enhance joint performance. The developed simulation software is expected to give indicative results as well as testing different types of prosthetic implant. Design parameterization and sensitivity analysis for geometrical features are discussed. Thus, an integrated environment is proposed to link the real-time simulation software with a manufacturing environment so as to assist the production of patient specific implants by rapid manufacturing

Reducing redundancy of real time computer graphics in mobile systems

The goal of this thesis is to propose novel and effective techniques to eliminate redundant computations that waste energy and are performed in real-time computer graphics applications, with special focus on mobile GPU micro-architecture. Improving the energy-efficiency of CPU/GPU systems is not only key to enlarge their battery life, but also allows to increase their performance because, to avoid overheating above thermal limits, SoCs tend to be throttled when the load is high for a large period of time. Prior studies pointed out that the CPU and especially the GPU are the principal energy consumers in the graphics subsystem, being the off-chip main memory accesses and the processors inside the GPU the primary energy consumers of the graphics subsystem. First, we focus on reducing redundant fragment processing computations by means of improving the culling of hidden surfaces. During real-time graphics rendering, objects are processed by the GPU in the order they are submitted by the CPU, and occluded surfaces are often processed even though they will end up not being part of the final image. When the GPU realizes that an object or part of it is not going to be visible, all activity required to compute its color and store it has already been performed. We propose a novel architectural technique for mobile GPUs, Visibility Rendering Order (VRO), which reorders objects front-to-back entirely in hardware to maximize the culling effectiveness of the GPU and minimize overshading, hence reducing execution time and energy consumption. VRO exploits the fact that the objects in graphics animated applications tend to keep its relative depth order across consecutive frames (temporal coherence) to provide the feeling of smooth transition. VRO keeps visibility information of a frame, and uses it to reorder the objects of the following frame. VRO just requires adding a small hardware to capture the visibility information and use it later to guide the rendering of the following frame. Moreover, VRO works in parallel with the graphics pipeline, so negligible performance overheads are incurred. We illustrate the benefits of VRO using various unmodified commercial 3D applications for which VRO achieves 27% speed-up and 14.8% energy reduction on average. Then, we focus on avoiding redundant computations related to CPU Collision Detection (CD). Graphics applications such as 3D games represent a large percentage of downloaded applications for mobile devices and the trend is towards more complex and realistic scenes with accurate 3D physics simulations. CD is one of the most important algorithms in any physics kernel since it identifies the contact points between the objects of a scene and determines when they collide. However, real-time accurate CD is very expensive in terms of energy consumption. We propose Render Based Collision Detection (RBCD), a novel energy-efficient high-fidelity CD scheme that leverages some intermediate results of the rendering pipeline to perform CD, so that redundant tasks are done just once. Comparing RBCD with a conventional CD completely executed in the CPU, we show that its execution time is reduced by almost three orders of magnitude (600x speedup), because most of the CD task of our model comes for free by reusing the image rendering intermediate results. Although not necessarily, such a dramatic time improvement may result in better frames per second if physics simulation stays in the critical path. However, the most important advantage of our technique is the enormous energy savings that result from eliminating a long and costly CPU computation and converting it into a few simple operations executed by a specialized hardware within the GPU. Our results show that the energy consumed by CD is reduced on average by a factor of 448x (i.e., by 99.8\%). These dramatic benefits are accompanied by a higher fidelity CD analysis (i.e., with finer granularity), which improves the quality and realism of the application.El objetivo de esta tesis es proponer técnicas efectivas y originales para eliminar computaciones inútiles que aparecen en aplicaciones gráficas, con especial énfasis en micro-arquitectura de GPUs. Mejorar la eficiencia energética de los sistemas CPU/GPU no es solo clave para alargar la vida de la batería, sino también incrementar su rendimiento. Estudios previos han apuntado que la CPU y especialmente la GPU son los principales consumidores de energía en el sub-sistema gráfico, siendo los accesos a memoria off-chip y los procesadores dentro de la GPU los principales consumidores de energía del sub-sistema gráfico. Primero, nos hemos centrado en reducir computaciones redundantes de la fase de fragment processing mediante la mejora en la eliminación de superficies ocultas. Durante el renderizado de gráficos en tiempo real, los objetos son procesados por la GPU en el orden en el que son enviados por la CPU, y las superficies ocultas son a menudo procesadas incluso si no no acaban formando parte de la imagen final. Cuando la GPU averigua que el objeto o parte de él no es visible, toda la actividad requerida para computar su color y guardarlo ha sido realizada. Proponemos una técnica arquitectónica original para GPUs móviles, Visibility Rendering Order (VRO), la cual reordena los objetos de delante hacia atrás por completo en hardware para maximizar la efectividad del culling de la GPU y así minimizar el overshading, y por lo tanto reducir el tiempo de ejecución y el consumo de energía. VRO explota el hecho de que los objetos de las aplicaciones gráficas animadas tienden a mantener su orden relativo en profundidad a través de frames consecutivos (coherencia temporal) para proveer animaciones con transiciones suaves. Dado que las relaciones de orden en profundidad entre objetos son testeadas en la GPU, VRO introduce costes mínimos en energía. Solo requiere añadir una pequeña unidad hardware para capturar la información de visibilidad. Además, VRO trabaja en paralelo con el pipeline gráfico, por lo que introduce costes insignificantes en tiempo. Ilustramos los beneficios de VRO usango varias aplicaciones 3D comerciales para las cuales VRO consigue un 27% de speed-up y un 14.8% de reducción de energía en media. En segundo lugar, evitamos computaciones redundantes relacionadas con la Detección de Colisiones (CD) en la CPU. Las aplicaciones gráficas animadas como los juegos 3D representan un alto porcentaje de las aplicaciones descargadas en dispositivos móviles y la tendencia es hacia escenas más complejas y realistas con simulaciones físicas 3D precisas. La CD es uno de los algoritmos más importantes entre los kernel de físicas dado que identifica los puntos de contacto entre los objetos de una escena. Sin embargo, una CD en tiempo real y precisa es muy costosa en términos de consumo energético. Proponemos Render Based Collision Detection (RBCD), una técnica energéticamente eficiente y preciso de CD que utiliza resultados intermedios del rendering pipeline para realizar la CD. Comparando RBCD con una CD convencional completamente ejecutada en la CPU, mostramos que el tiempo de ejecución es reducido casi tres órdenes de magnitud (600x speedup), porque la mayoría de la CD de nuestro modelo reusa resultados intermedios del renderizado de la imagen. Aunque no es así necesariamente, esta espectacular en tiempo puede resultar en mejores frames por segundo si la simulación de físicas está en el camino crítico. Sin embargo, la ventaja más importante de nuestra técnica es el enorme ahorro de energía que resulta de eliminar las largas y costosas computaciones en la CPU, sustituyéndolas por unas pocas operaciones ejecutadas en un hardware especializado dentro de la GPU. Nuestros resultados muestran que la energía consumida por la CD es reducidad en media por un factor de 448x. Estos dramáticos beneficios vienen acompañados de una mayor fidelidad en la CD (i.e. con granularidad más fina)Postprint (published version

Virtual Reality Simulation of Glenoid Reaming Procedure

Glenoid reaming is a bone machining operation in Total Shoulder Arthroplasty (TSA) in which the glenoid bone is resurfaced to make intimate contact with implant undersurface. While this step is crucial for the longevity of TSA, many surgeons find it technically challenging. With the recent advances in Virtual Reality (VR) simulations, it has become possible to realistically replicate complicated operations without any need for patients or cadavers, and at the same time, provide quantitative feedback to improve surgeons\u27 psycho-motor skills. In light of these advantages, the current thesis intends to develop tools and methods required for construction of a VR simulator for glenoid reaming, in an attempt to construct a reliable tool for preoperative training and planning for surgeons involved with TSA. Towards the end, this thesis presents computational algorithms to appropriately represent surgery tool and bone in the VR environment, determine their intersection and compute realistic haptic feedback based on the intersections. The core of the computations is constituted by sampled geometrical representations of both objects. In particular, point cloud model of the tool and voxelized model of bone - that is derived from Computed Tomography (CT) images - are employed. The thesis shows how to efficiently construct these models and adequately represent them in memory. It also elucidates how to effectively use these models to rapidly determine tool-bone collisions and account for bone removal momentarily. Furthermore, the thesis applies cadaveric experimental data to study the mechanics of glenoid reaming and proposes a realistic model for haptic computations. The proposed model integrates well with the developed computational tools, enabling real-time haptic and graphic simulation of glenoid reaming. Throughout the thesis, a particular emphasis is placed upon computational efficiency, especially on the use of parallel computing using Graphics Processing Units (GPUs). Extensive implementation results are also presented to verify the effectiveness of the developments. Not only do the results of this thesis advance the knowledge in the simulation of glenoid reaming, but they also rigorously contribute to the broader area of surgery simulation, and can serve as a step forward to the wider implementation of VR technology in surgeon training programs

Technologies for Biomechanically-Informed Image Guidance of Laparoscopic Liver Surgery

Laparoscopic surgery for liver resection has a number medical advantages over open surgery, but also comes with inherent technical challenges. The surgeon only has a very limited field of view through the imaging modalities routinely employed intra-operatively, laparoscopic video and ultrasound, and the pneumoperitoneum required to create the operating space and gaining access to the organ can significantly deform and displace the liver from its pre-operative configuration. This can make relating what is visible intra-operatively to the pre-operative plan and inferring the location of sub-surface anatomy a very challenging task. Image guidance systems can help overcome these challenges by updating the pre-operative plan to the situation in theatre and visualising it in relation to the position of surgical instruments. In this thesis, I present a series of contributions to a biomechanically-informed image-guidance system made during my PhD. The most recent one is work on a pipeline for the estimation of the post-insufflation configuration of the liver by means of an algorithm that uses a database of segmented training images of patient abdomens where the post-insufflation configuration of the liver is known. The pipeline comprises an algorithm for inter and intra-subject registration of liver meshes by means of non-rigid spectral point-correspondence finding. My other contributions are more fundamental and less application specific, and are all contained and made available to the public in the NiftySim open-source finite element modelling package. Two of my contributions to NiftySim are of particular interest with regards to image guidance of laparoscopic liver surgery: 1) a novel general purpose contact modelling algorithm that can be used to simulate contact interactions between, e.g., the liver and surrounding anatomy; 2) membrane and shell elements that can be used to, e.g., simulate the Glisson capsule that has been shown to significantly influence the organ’s measured stiffness

A biomechanics-based articulation model for medical applications

Computer Graphics came into the medical world especially after the arrival of 3D medical imaging. Computer Graphics techniques are already integrated in the diagnosis procedure by means of the visual tridimensional analysis of computer tomography, magnetic resonance and even ultrasound data. The representations they provide, nevertheless, are static pictures of the patients' body, lacking in functional information. We believe that the next step in computer assisted diagnosis and surgery planning depends on the development of functional 3D models of human body. It is in this context that we propose a model of articulations based on biomechanics. Such model is able to simulate the joint functionality in order to allow for a number of medical applications. It was developed focusing on the following requirements: it must be at the same time simple enough to be implemented on computer, and realistic enough to allow for medical applications; it must be visual in order for applications to be able to explore the joint in a 3D simulation environment. Then, we propose to combine kinematical motion for the parts that can be considered as rigid, such as bones, and physical simulation of the soft tissues. We also deal with the interaction between the different elements of the joint, and for that we propose a specific contact management model. Our kinematical skeleton is based on anatomy. Special considerations have been taken to include anatomical features like axis displacements, range of motion control, and joints coupling. Once a 3D model of the skeleton is built, it can be simulated by data coming from motion capture or can be specified by a specialist, a clinician for instance. Our deformation model is an extension of the classical mass-spring systems. A spherical volume is considered around mass points, and mechanical properties of real materials can be used to parameterize the model. Viscoelasticity, anisotropy and non-linearity of the tissues are simulated. We particularly proposed a method to configure the mass-spring matrix such that the objects behave according to a predefined Young's modulus. A contact management model is also proposed to deal with the geometric interactions between the elements inside the joint. After having tested several approaches, we proposed a new method for collision detection which measures in constant time the signed distance to the closest point for each point of two meshes subject to collide. We also proposed a method for collision response which acts directly on the surfaces geometry, in a way that the physical behavior relies on the propagation of reaction forces produced inside the tissue. Finally, we proposed a 3D model of a joint combining the three elements: anatomical skeleton motion, biomechanical soft tissues deformation, and contact management. On the top of that we built a virtual hip joint and implemented a set of medical applications prototypes. Such applications allow for assessment of stress distribution on the articular surfaces, range of motion estimation based on ligament constraint, ligament elasticity estimation from clinically measured range of motion, and pre- and post-operative evaluation of stress distribution. Although our model provides physicians with a number of useful variables for diagnosis and surgery planning, it should be improved for effective clinical use. Validation has been done partially. However, a global clinical validation is necessary. Patient specific data are still difficult to obtain, especially individualized mechanical properties of tissues. The characterization of material properties in our soft tissues model can also be improved by including control over the shear modulus

Dynamiksimulation in der Computergraphik

Die interaktive physikalisch-basierte Simulation von Starrkörpern und deformierbaren Festkörpern ist ein wichtiges und aktuelles Forschungsgebiet in der Computergraphik und ein essentieller Bestandteil in vielen Anwendungen, wie z.B. Virtual Prototyping, Computerspiele oder Trainingssimulatoren. In dieser Arbeit werden interaktive Simulationsmethoden für Mehrkörpersysteme, Textilien und inkompressible deformierbare Volumenkörper vorgestellt