<p>Computer-based surgical simulation and non-rigid medical image registration in image-guided interventions are examples of applications that would benefit from real-time deformation simulation of soft tissues. The physics of deformation for biological soft-tissue is best described by nonlinear continuum mechanics-based models which then can be discretized by the Finite Element Method (FEM) for a numerical solution. Computational complexity of nonlinear FEM-based models has limited their use in real-time applications. The data-parallel nature and intense arithmetic operations in nonlinear FEM models are suitable for massive parallelization of the computations, in order to meet the response time requirements in such applications.</p> <p>This thesis is concerned with computational aspects of complex nonlinear deformation analysis problems with an emphasis on the speed of response using a parallel computing philosophy. It proposes a fast, accurate and scalable Graphic Processing Unit (GPU)-based implementation of the total Lagrangian FEM using implicit time integration for dynamic nonlinear deformation analysis. This is a general formulation valid for large deformations and strains and can account for material nonlinearities. A penalty method is used to satisfy the physical boundary constraints due to contact between deformable objects. The proposed set of optimized GPU kernels for computing the FEM matrices achieves more than 100 GFLOPS on a GTX 470 GPU device. The use of a novel vector assembly kernel and memory optimization strategies result in a performance gain of up to 25 GFLOPS in the PCG computations.</p> / Doctor of Philosophy (PhD)

No description available.

O objetivo deste estudo foi comparar o eixo de rotação verdadeiro com o anatômico em ambiente virtual 3D, e seus efeitos sobre dois pontos anatômicos mandibulares. O eixo verdadeiro foi determinado em 14 indivíduos por meio de axiografia, e transferido para o ambiente virtual por TCFC, e posteriormente determinado anatomicamente, onde foram medidas as distâncias entre ambos. Foram simuladas rotações de 2º, 5º e 8º da mandíbula nos dois eixos, tanto para abertura como fechamento, e quantificadas as diferenças nos pontos da linha média inferior (LMI) e pogônio (Pg). O teste t pareado foi utilizado para examinar as diferenças entre as médias nas posições desses pontos (p<0,05). Os eixos verdadeiros localizaram-se dentro de um raio de 5 mm do anatômico em 67,86% da amostra. A distância absoluta média entre os eixos foi de 4,79 mm, enquanto que a vetorial foi de 2,33 no plano horizontal e 3,03 mm no vertical, resultando na direção anteroinferior em 71,43% dos eixos verdadeiros. Houve diferença estatisticamente significante na posição dos pontos LMI e Pg para todas as magnitudes e direções, entre os eixos. O eixo verdadeiro está localizado na direção anteroinferior em relação ao anatômico. Os efeitos na mandíbula são significantes e diferentes em todas as amplitudes, tanto para abertura como fechamento, porém com possível pequena relevância clínica. / The aim of this study was to compare the true hinge axis to the anatomic one in a virtual 3D environment, and also their respective effects on two mandibular anatomic points. The true axis has been determined in 14 individuals by means of axiography, and later transferred to a virtual environment by CBTC, where the anatomical axis was determined, and measured the distances between them. Mandibular rotation of 2º, 5º and 8º in both axes were performed, both for opening and closing, as well as the quantification of the difference found in the points of the lower midline (LM) and pogonion (Pg). Paired t-test was used to examine differences between the average values in the position of those points (p<0,05). The true axis was located within a 5mm-radius of the anatomic axis throughout 67.86% of the sample. The average absolute distance between the axes was 4.79 mm, while the vector distance was 2.33 mm in the horizontal plane e 3.03mm in the vertical plane, amounting to an anteriorinferior direction of 71.43% of the true axis. There was significant difference in the position of points LM and Pg to all magnitudes and directions within the axes. The true hinge axis is located in the anterior-inferior direction in relation to the anatomic axis. The effects observed onto the mandible are significant and different in all amplitudes, both for opening and closing positions, however they present small clinical relevance.

In this dissertation, the accuracy and reliability of non-linear finite element computations in application to surgical simulation is evaluated. The evaluation is performed through comparison between the experiment and finite element analysis of indentation of soft tissue phantom and human brain phantom. The evaluation is done in terms of the forces acting on the cylindrical Aluminium indenter and deformation of the phantoms due to these forces. The deformation of the phantoms is measured by tracking 3D motions of X-ray opaque markers implanted in the direct neighbourhood under the indenter using a custom-made biplane X-ray image intensifiers (XRII) system. The phantoms are made of Sylgard® 527 gel to simulate the hyperelastic constitutive behaviour of the brain tissue. The phantoms are prepared layer by layer to facilitate the implantation of the X-ray opaque markers. The modelling of soft tissue phantom indentation and human brain phantom indentation is performed using the ABAQUSTM/Standard finite element solver. Realistic geometry model of the human brain phantom obtained from Magnetic Resonance images is used. Specific constitutive properties of the phantom layers determined through uniaxial compression tests are used in the model. The models accurately predict the indentation force-displacement relations and marker displacements in both soft tissue phantom indentation and human brain phantom indentation. Good agreement between the experimental and modelling results verifies the reliability and accuracy of the finite element analysis techniques used in this study and confirms the predictive power of these techniques in application to surgical simulation.

O objetivo deste estudo foi comparar o eixo de rotação verdadeiro com o anatômico em ambiente virtual 3D, e seus efeitos sobre dois pontos anatômicos mandibulares. O eixo verdadeiro foi determinado em 14 indivíduos por meio de axiografia, e transferido para o ambiente virtual por TCFC, e posteriormente determinado anatomicamente, onde foram medidas as distâncias entre ambos. Foram simuladas rotações de 2º, 5º e 8º da mandíbula nos dois eixos, tanto para abertura como fechamento, e quantificadas as diferenças nos pontos da linha média inferior (LMI) e pogônio (Pg). O teste t pareado foi utilizado para examinar as diferenças entre as médias nas posições desses pontos (p<0,05). Os eixos verdadeiros localizaram-se dentro de um raio de 5 mm do anatômico em 67,86% da amostra. A distância absoluta média entre os eixos foi de 4,79 mm, enquanto que a vetorial foi de 2,33 no plano horizontal e 3,03 mm no vertical, resultando na direção anteroinferior em 71,43% dos eixos verdadeiros. Houve diferença estatisticamente significante na posição dos pontos LMI e Pg para todas as magnitudes e direções, entre os eixos. O eixo verdadeiro está localizado na direção anteroinferior em relação ao anatômico. Os efeitos na mandíbula são significantes e diferentes em todas as amplitudes, tanto para abertura como fechamento, porém com possível pequena relevância clínica. / The aim of this study was to compare the true hinge axis to the anatomic one in a virtual 3D environment, and also their respective effects on two mandibular anatomic points. The true axis has been determined in 14 individuals by means of axiography, and later transferred to a virtual environment by CBTC, where the anatomical axis was determined, and measured the distances between them. Mandibular rotation of 2º, 5º and 8º in both axes were performed, both for opening and closing, as well as the quantification of the difference found in the points of the lower midline (LM) and pogonion (Pg). Paired t-test was used to examine differences between the average values in the position of those points (p<0,05). The true axis was located within a 5mm-radius of the anatomic axis throughout 67.86% of the sample. The average absolute distance between the axes was 4.79 mm, while the vector distance was 2.33 mm in the horizontal plane e 3.03mm in the vertical plane, amounting to an anteriorinferior direction of 71.43% of the true axis. There was significant difference in the position of points LM and Pg to all magnitudes and directions within the axes. The true hinge axis is located in the anterior-inferior direction in relation to the anatomic axis. The effects observed onto the mandible are significant and different in all amplitudes, both for opening and closing positions, however they present small clinical relevance.

The goal of this project was to evaluate the viability of a mass-spring-damper based model for modeling of biological tissue. A method for automatically generating such a model from data taken from 3D medical imaging equipment including both the generation of point masses and an algorithm for generating the spring-damper links between these points is presented. Furthermore, an implementation of a simulation of this model running in real-time by utilizing the parallel computational power of modern GPU hardware through OpenCL is described. This implementation uses the fourth order Runge-Kutta method to improve stability over similar implementations. The difficulty of maintaining stability while still providing rigidness to the simulated tissue is thoroughly discussed. Several observations on the influence of the structure of the model on the consistency of the simulated tissue are also presented. This implementation also includes two manipulation tools, a move tool and a cut tool for interaction with the simulation. From the results, it is clear that the mass-springdamper model is a viable model that is possible to simulate in real-time on modern but commoditized hardware. With further development, this can be of great benefit to areas such as medical visualization and surgical simulation. / Målet med detta projekt var att utvärdera huruvida en modell baserad på massa-fjäderdämpare är meningsfull för att modellera biologisk vävnad. En metod för att automatiskt generera en sådan modell utifrån data tagen från medicinsk 3D-skanningsutrustning presenteras. Denna metod inkluderar både generering av punktmassor samt en algoritm för generering av länkar mellan dessa. Vidare beskrivs en implementation av en simulering av denna modell som körs i realtid genom att utnyttja den parallella beräkningskraften hos modern GPU-hårdvara via OpenCL. Denna implementation använder sig av fjärde ordningens Runge-Kutta-metod för förbättrad stabilitet jämfört med liknande implementationer. Svårigheten att bibehålla stabiliteten samtidigt som den simulerade vävnaden ges tillräcklig styvhet diskuteras genomgående. Flera observationer om modellstrukturens inverkan på den simulerade vävnadens konsistens presenteras också. Denna implementation inkluderar två manipuleringsverktyg, ett flytta-verktyg och ett skärverktyg för att interagera med simuleringen. Resultaten visar tydligt att en modell baserad på massa-fjäder-dämpare är en rimlig modell som är möjlig att simulera i realtid på modern men lättillgänglig hårdvara. Med vidareutveckling kan detta bli betydelsefullt för områden så som medicinsk bildvetenskap och kirurgisk simulering.