Modern medical imaging devices are able to generate highly detailed three-dimensional (3D) images of the skeleton. Computerized image processing and analysis methods, combined with real-time volume visualization techniques, can greatly facilitate the interpretation of such images and are increasingly used in surgical planning to aid reconstruction of the skeleton after trauma or disease. Two key challenges are to accurately separate (segment) bone structures or cavities of interest from the rest of the image and to interact with the 3D data in an efficient way. This thesis presents efficient and precise interactive methods for segmenting, visualizing, and analysing 3D computed tomography (CT) images of the skeleton. The methods are validated on real CT datasets and are primarily intended to support planning and evaluation of cranio-maxillofacial (CMF) and orthopedic surgery. Two interactive methods for segmenting the orbit (eye-socket) are introduced. The first method implements a deformable model that is guided and fitted to the orbit via haptic 3D interaction, whereas the second method implements a user-steered volumetric brush that uses distance and gradient information to find exact object boundaries. The thesis also presents a semi-automatic method for measuring 3D angulation changes in wrist fractures. The fractured bone is extracted with interactive mesh segmentation, and the angulation is determined with a technique based on surface registration and RANSAC. Lastly, the thesis presents an interactive and intuitive tool for segmenting individual bones and bone fragments. This type of segmentation is essential for virtual surgery planning, but takes several hours to perform with conventional manual methods. The presented tool combines GPU-accelerated random walks segmentation with direct volume rendering and interactive 3D texture painting to enable quick marking and separation of bone structures. It enables the user to produce an accurate segmentation within a few minutes, thereby removing a major bottleneck in the planning procedure.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

AIM: Extraction of a tooth can lead to alveolar ridge resorption which can be minimized by socket preservation. The aim of this study is to analyze vertical and horizontal alveolar ridge dimensions clinically and by CBCT immediately following extraction and 3-4 months following socket preservation. METHODS: The preserved group (P) consisted of 20 patients with1-2 non-molar teeth requiring extraction with socket preservation, while the control group (C) consisted of 5 patients requiring extraction alone. An acrylic stent was fabricated presurgically in order to measure vertical and horizontal ridge dimensions clinically and radiographically immediately following extraction and 3-4 months following socket preservation. RESULTS: Overall, P sites gained ridge height and lost minimal ridge width over 3-4 months, while C sites lost both ridge height and width. Preserved sites in which the teeth were extracted due to caries had the most significant gain in the radiographic vertical occlusal dimension (RVO). Overall, high correlations were found between the clinical and radiographic measurements at the initial surgery and at the 3-4 month follow up. CONCLUSIONS: The preserved group had minimal ridge resorption and more socket bony fill when compared to the non-preserved group 3-4 months following tooth extraction, especially when the tooth was extracted due to caries. Additionally, the CBCT can be a useful diagnostic tool to evaluate socket preservation healing, as it compares well to clinical assessments of socket healing.

Accurate and automatic segmentation techniques that do not require any explicit prior model have been of high interest in the medical community. We propose a fully-automatic method for segmenting the femur from 3D Computed Tomography scans, based on the graph-cut segmentation framework and the bone boundary enhancement filter analyzing second-order local structures. The presented algorithm is evaluated in large-scale experiments, conducted on 197 CT volumes, and compared to other three automatic bone segmentation methods. Out of the four tested approaches, the proposed algorithm achieved most accurate results and segmented the femur correctly in 81% of the cases.

<p>X-ray computed tomography (CT) is a non-invasive medical imaging technique that generates cross-sectional images by acquiring attenuation-based projection measurements at multiple angles. Since its first introduction in the 1970s, substantial technical improvements have led to the expanding use of CT in clinical examinations. CT has become an indispensable imaging modality for the diagnosis of a wide array of diseases in both pediatric and adult populations [1, 2]. Currently, approximately 272 million CT examinations are performed annually worldwide, with nearly 85 million of these in the United States alone [3]. Although this trend has decelerated in recent years, CT usage is still expected to increase mainly due to advanced technologies such as multi-energy [4], photon counting [5], and cone-beam CT [6].</p><p>Despite the significant clinical benefits, concerns have been raised regarding the population-based radiation dose associated with CT examinations [7]. From 1980 to 2006, the effective dose from medical diagnostic procedures rose six-fold, with CT contributing to almost half of the total dose from medical exposure [8]. For each patient, the risk associated with a single CT examination is likely to be minimal. However, the relatively large population-based radiation level has led to enormous efforts among the community to manage and optimize the CT dose.</p><p>As promoted by the international campaigns Image Gently and Image Wisely, exposure to CT radiation should be appropriate and safe [9, 10]. It is thus a responsibility to optimize the amount of radiation dose for CT examinations. The key for dose optimization is to determine the minimum amount of radiation dose that achieves the targeted image quality [11]. Based on such principle, dose optimization would significantly benefit from effective metrics to characterize radiation dose and image quality for a CT exam. Moreover, if accurate predictions of the radiation dose and image quality were possible before the initiation of the exam, it would be feasible to personalize it by adjusting the scanning parameters to achieve a desired level of image quality. The purpose of this thesis is to design and validate models to quantify patient-specific radiation dose prospectively and task-based image quality. The dual aim of the study is to implement the theoretical models into clinical practice by developing an organ-based dose monitoring system and an image-based noise addition software for protocol optimization. </p><p>More specifically, Chapter 3 aims to develop an organ dose-prediction method for CT examinations of the body under constant tube current condition. The study effectively modeled the anatomical diversity and complexity using a large number of patient models with representative age, size, and gender distribution. The dependence of organ dose coefficients on patient size and scanner models was further evaluated. Distinct from prior work, these studies use the largest number of patient models to date with representative age, weight percentile, and body mass index (BMI) range.</p><p>With effective quantification of organ dose under constant tube current condition, Chapter 4 aims to extend the organ dose prediction system to tube current modulated (TCM) CT examinations. The prediction, applied to chest and abdominopelvic exams, was achieved by combining a convolution-based estimation technique that quantifies the radiation field, a TCM scheme that emulates modulation profiles from major CT vendors, and a library of computational phantoms with representative sizes, ages, and genders. The prospective quantification model is validated by comparing the predicted organ dose with the dose estimated based on Monte Carlo simulations with TCM function explicitly modeled. </p><p>Chapter 5 aims to implement the organ dose-estimation framework in clinical practice to develop an organ dose-monitoring program based on a commercial software (Dose Watch, GE Healthcare, Waukesha, WI). In the first phase of the study we focused on body CT examinations, and so the patient’s major body landmark information was extracted from the patient scout image in order to match clinical patients against a computational phantom in the library. The organ dose coefficients were estimated based on CT protocol and patient size as reported in Chapter 3. The exam CTDIvol, DLP, and TCM profiles were extracted and used to quantify the radiation field using the convolution technique proposed in Chapter 4. </p><p>With effective methods to predict and monitor organ dose, Chapters 6 aims to develop and validate improved measurement techniques for image quality assessment. Chapter 6 outlines the method that was developed to assess and predict quantum noise in clinical body CT images. Compared with previous phantom-based studies, this study accurately assessed the quantum noise in clinical images and further validated the correspondence between phantom-based measurements and the expected clinical image quality as a function of patient size and scanner attributes. </p><p>Chapter 7 aims to develop a practical strategy to generate hybrid CT images and assess the impact of dose reduction on diagnostic confidence for the diagnosis of acute pancreatitis. The general strategy is (1) to simulate synthetic CT images at multiple reduced-dose levels from clinical datasets using an image-based noise addition technique; (2) to develop quantitative and observer-based methods to validate the realism of simulated low-dose images; (3) to perform multi-reader observer studies on the low-dose image series to assess the impact of dose reduction on the diagnostic confidence for multiple diagnostic tasks; and (4) to determine the dose operating point for clinical CT examinations based on the minimum diagnostic performance to achieve protocol optimization. </p><p>Chapter 8 concludes the thesis with a summary of accomplished work and a discussion about future research.</p> / Dissertation

O presente projeto consistiu no estudo e aplicação do algoritmo FDK (Feldkamp-Davis-Kress) para a reconstrução de imagens tomográficas utilizando a geometria de feixe cônico, resultando na implementação de um sistema adaptado de tomografia computadorizada multicortes (TCMC). Para a aquisição das projeções, utilizou-se uma plataforma giratória com goniômetro acoplado, um equipamento de raios X e um detector digital, tipo CCD. Para processar a reconstrução das imagens, foi utilizado um PC, no qual foi implementado o algoritmo FDK. Inicialmente foi aplicado o algoritmo FDK original, no qual se assume o caso físico ideal no processo de medições. Em seguida, foram incorporadas ao algoritmo, algumas correções de artefatos relacionados ao processo de medição das projeções. Para testar o funcionamento do algoritmo implementado, foram feitas reconstruções a partir de projeções simuladas computacionalmente. Foram montados e testados três sistemas de aquisição de projeções, nos quais foram usados diferentes equipamentos de raios X, detectores, metodologias e técnicas radiográficas, a fim de garantir que fossem coletados os melhores conjuntos possíveis de projeções. Realizou-se a calibração do sistema de TCMC implementado. Para isso, utilizou-se um objeto com uma distribuição de coeficientes de atenuação linear conhecida, que foi projetado e fabricado especificamente para isto. Por fim, o sistema de TCMC implementado foi utilizado na reconstrução tomográfica de um objeto não homogêneo, cuja distribuição volumétrica do coeficiente de atenuação linear é desconhecida. As imagens reconstruídas foram analisadas a fim de avaliar o desempenho do sistema de TCMC implementado. / This work consisted on the study and application of the FDK (Feldkamp-Davis-Kress) algorithm for tomographic image reconstruction using cone-beam geometry, resulting on the implementation of an adapted multi-slice computed tomography (MSCT) system. For the acquisition of the projections, a rotating platform coupled to a goniometer, an x-ray equipment and a CCD type digital detector were used. The FDK algorithm was implemented on a PC which was used for the reconstruction process. Initially, the original FDK algorithm was applied considering only the ideal physical conditions in the measurement process. Then some artifacts corrections related to the projections measurement process were incorporated. Computational simulations were performed to test the functioning of the implemented algorithm. Three projections acquisition systems, which used different x-ray equipments, detectors, methodologies and radiographic techniques, were assembled and tested in order to ensure that the best possible set of data was collected. The implemented MSCT system was calibrated. A specially designed and manufactured object with a known linear attenuation coefficient distribution was used for this purpose. Finally, the implemented MSCT system was used for multi-slice tomographic reconstruction of an inhomogeneous object, whose attenuation coefficient distribution was unknown. The reconstructed images were analyzed to assess the performance of the TCMC system that was implemented.

INTRODUÇÃO: A doença de Chagas (DCh) representa um grave problema de saúde pública na maioria dos países da América Latina. Sintomatologia frequente, a dor torácica ou precordial em pacientes com DCh pode assemelhar-se àquela observada na doença arterial coronária (DAC), constituindo-se, dessa forma, em desafio diagnóstico para os clínicos. A frequência da DAC em pacientes com DCh continua indefinida na literatura, permanecendo a hipótese de que pacientes com DCh possam apresentar menor proporção de DAC. A angiografia coronária por tomografia computadorizada (ATC), em aparelho de múltiplas colunas de detectores, é um método não invasivo de alta acurácia que permite o diagnóstico precoce de placas ateromatosas, obstrutivas ou não, e que poderia detectar a frequência de DAC neste grupo de pacientes. OBJETIVO: Investigar a presença de aterosclerose coronária em pacientes com DCh, comparando com um grupo controle de indivíduos assintomáticos e sem doença coronária conhecida, utilizando a angiografia coronária por tomografia computadorizada. MÉTODOS: Foram estudados 43 pacientes portadores da DCh, sendo 16 (37,2%) homens. O grupo controle foi composto por 66 indivíduos não portadores da DCh, sendo 28 (42,4%) homens. Os grupos foram pareados pelo escore de risco de Framingham, respeitando-se a mesma faixa de risco (baixo, intermediário e alto), além do pareamento por sexo e faixa etária. Os exames foram realizados em tomografia computadorizada de 320 colunas de detectores e o diagnóstico de DAC foi definido pela presença de placa aterosclerótica, mesmo sem causar obstrução luminal. DAC obstrutiva significativa foi considerada pela presença de ao menos uma placa causando redução maior do que 50% do diâmetro da luz arterial. RESULTADOS: Foram observadas diferenças significativas nos parâmetros relacionados à DAC, sendo sua frequência significativamente menor nos pacientes portadores da DCh. A presença de DAC foi observada em 9 indivíduos (20,9%) portadores da DCh e em 32 indivíduos do grupo controle (48,5%), com p=0,004. A magnitude da estenose coronária foi significativamente menor nos pacientes com DCh que nos controles na análise por paciente, por território e por segmentos coronários (p<0,001, p=0,012 e p=0,045, respectivamente). CONCLUSÕES: Os pacientes portadores da DCh apresentam baixa frequência de DAC definida pela tomografia computadorizada de artérias coronárias. A frequência de DAC, obstrutiva ou não, em pacientes com DCh foi significativamente menor que a observada no grupo controle de pacientes sem DAC prévia conhecida / INTRODUCTION: Chagas disease (CD) is a serious public health problem in most of Latin American countries. Precordial or chest pain in patients with CD is a frequent symptom and can be similar to that observed in coronary artery disease (CAD), what represents a diagnostic challenge to the physicians. The frequency of CAD in patients with CD continues undefined in the literature, remaining the hypothesis that patients with CD could present a lower proportion of CAD. Computed tomography angiography (CTA) is a high accuracy and non-invasive method that allows an early diagnostic of atherosclerotic plaque, obstructive or not, and that could detect the frequency of CAD in this group of patients. OBJECTIVE: Investigate coronary atherosclerosis by CTA in patients with CD, comparing with an asymptomatic control group without known CAD. METHODS: 43 patients with CD were studied and 16 (37.2%) were men. The control group was composed by 66 non-carriers of CD and 28 (42.4%) were men. The groups were matched for Framingham risk score (low, medium and high) as well as sex and age. The exams were performed in 320-multidetector rows CT and the CAD diagnostic was defined as the presence of atherosclerotic plaques, even without luminal obstruction. Significant obstructive CAD was considered if at least one plaque was present causing more than 50% of reduction in the arterial lumen diameter. RESULTS: Significant differences were observed in parameters related to CAD, showing lower frequency of CAD in patients with CD. The presence of CAD was observed in 9 patients (20.9%) with CD and in 32 patients (48.5%) from the control group, with p=0.004. The magnitude of coronary stenosis was significantly lower in patients with CD than in controls, in a per patient, per territory and per segment coronary analyses (p<0.001, p=0.012 e p=0.045, respectively). CONCLUSIONS: Patients with CD have a low frequency of CAD defined by coronary CTA. The CAD frequency, obstructive or not, in patients with CD was significantly lower than the observed in the control group without known CAD

O objetivo deste estudo foi comparar, por meio de tomografia computadorizada de feixe cônico, a inclinação axial dos dentes posteriores e a morfologia óssea alveolar mandibular entre indivíduos com diferentes padrões faciais. Para isso, foram utilizadas 58 tomografias de indivíduos maiores de 14 anos de idade não tratados ortodonticamente. Os indivíduos foram divididos em 3 grupos de acordo com o padrão facial avaliado pelo índice VERT de Ricketts: Grupo 1: composto por 18 indivíduos com padrão braquifacial, com idade média de 21,58 anos (d.p.=7,43); Grupo 2: composto por 23 indivíduos com padrão mesofacial, com idade média de 19,14 anos (d.p.=5,19); e Grupo 3: composto por 17 indivíduos com padrão dolicofacial, com idade média de 19,09 anos (d.p.=6,89). Foi realizada uma avaliação quantitativa das tábuas ósseas vestibular e lingual dos dentes pósteroinferiores, em tomografias de feixe cônico. As medidas utilizadas foram: altura do osso mandibular vestibular e lingual, largura mandibular cervical e média, inclinação mandibular, inclinação da face vestibular, largura do molar, angulação do molar e ângulo dente/osso. A comparação intergrupos foi realizada com a utilização do teste ANOVA a um critério de seleção e teste de Tukey quando necessário. Para verificar se existe correlação entre o padrão facial e as variáveis estudadas foi utilizado o teste de correlação de Pearson. Os resultados demonstraram que os indivíduos braquifaciais apresentaram uma menor inclinação mandibular quando comparados aos indivíduos mesofaciais e dolicofaciais. Houve diferença significante da altura mandibular vestibular entre os três grupos avaliados, sendo que esta foi menor no grupo braquifacial, intermediária no grupo mesofacial e maior no grupo dolicofacial. A altura mandibular lingual foi menor no grupo braquifacial em comparação aos grupos mesofacial e dolicofacial. A largura mandibular média foi maior nos indivíduos braquifaciais em relação aos mesofaciais. / The aim of this study was to compare, with cone beam computed tomography, the axial inclination of posterior teeth and mandibular alveolar bone morphology among individuals with different facial patterns. For this, 58 CT scans of untreated individuals orthodontically aged more than 14 years were used. The subjects were divided into 3 groups according to the facial pattern evaluated by the VERT index by Ricketts: Group 1 comprised 18 individuals with brachyfacial pattern, with a mean age of 21.58 years (s.d.=7.43); Group 2 comprised 23 individuals with mesofacial pattern, with a mean age of 19.14 years (s.d.=5.19); and Group 3 comprised 17 individuals with dolichofacial pattern, with a mean age of 19.09 years (s.d.=6.89). A quantitative assessment of the buccal and lingual bone plates of the mandibular posterior teeth were made in cone beam CT scans. The variables measured were: buccal and lingual mandibular height, cervical and middle mandibular width, mandibular inclination, inclination of the buccal surface, molar width, molar angle and tooth/bone angle. The intergroup comparison was performed by one-way ANOVA and Tukey test when necessary. To check whether there is a correlation between facial pattern and the variables studied, the Pearson correlation test was used. The results showed that the brachyfacial subjects had a smaller mandibular angle when compared to mesofacial and dolichofacial individuals. There was significant difference in the buccal mandibular height between the three groups, and this was smaller in the brachyfacial group, intermediate in the mesofacial group and larger in the dolichofacial group. Lingual mandibular height was smaller in brachyfacial group when compared to mesofacial and dolichofacial groups. The mean mandibular width was greater in brachyfacial than in mesofacial subjects.

Desde a invenção da tomografia computadorizada (CT) nos anos 70, toda década trouxe novas tecnologias para esta modalidade. Com estes avanços, também surgiu a necessidade de novas e melhores técnicas de avaliação de desempenho e segurança dos equipamentos de CT. Hoje, o controle de qualidade de equipamentos de CT é, em grande parte, feito manualmente. Portanto, é lento e, em parte, subjetivo. Neste trabalho, um software foi escrito em MatLab® para processar imagens do phantom de CT Catphan500®, aperfeiçoando a rotina do programa de controle de qualidade de CT. Com pouca interferência do usuário, o software mede a espessura de corte, incremento entre cortes e tamanho de pixel, avalia a linearidade do número CT, estima a Função Transferência de Modulação (MTF), o ruído e o Espectro de Potência do Ruído (NPS). Para a validação do software, conjuntos de imagens do phantom foram obtidas em 10 equipamentos de CT diferentes, com 27 protocolos diferentes. Cada conjunto foi analisado pelo software, e os resultados obtidos foram comparados aos resultados previamente obtidos pela rotina normal do programa controle de qualidade. Para essa comparação, dois testes de hipótese foram empregados: o teste t de Student (para os valores de espessura de corte, incremento entre cortes, tamanho de pixel e os coeficientes da avaliação de linearidade do número CT, adotando um valor-p de 0,01) e o teste F de Fisher (para o ruído, valor-p de 0,05). As funções MTF e NPS atualmente não são medidas na rotina do controle de qualidade, portanto não há resultado prévio para fazer esta comparação. Ao invés disso, o NPS foi ajustado em função da MTF (através da relação teórica que há entre os dois) e a qualidade do ajuste foi avaliada pelo teste de qui-quadrado. Dos 101 valores de t e 25 valores de F calculados, 2 e 1 respectivamente estavam fora do intervalo de aceitação. Este resultado está de acordo com os valores-p escolhidos e, portanto, os resultados obtidos pelo software estão de acordo com os resultados da rotina de controle de qualidade convencional. Os ajustes de NPS e MTF obtiveram incertezas grandes nos parâmetros de ajuste (incertezas da mesma ordem de grandeza dos próprios parâmetros). Porém, a avaliação do qui-quadrado reduzido indica que os ajustes foram aceitáveis (com exceção de um, que mostrou uma anomalia no NPS medido e foi desconsiderado). Portanto, o NPS e MTF obtidos estão de acordo com a expectativa teórica. / Since the introduction of the CT scanner as a diagnostic imaging modality, the scientific community has seen new and more complex CT technologies. These improvements brought the need for new and improved techniques to evaluate the safety and performance of these scanners. Nowadays, the interpretation of images generated during the implementation of CT quality control procedures are done visually in much of the cases. Therefore, it is slow and partially subjective. In this work, a software was written in MatLab to process images of the Catphan500 CT phantom, in order to improve the CT quality control workflow and its accuracy. The software evaluate the slice thickness, slice increment, and pixel size, calculates the CT number linearity, and assesses the Modulation Transfer Function (MTF), the noise and the Noise Power Spectrum (NPS). Image sets of the phantom were obtained from 10 different scanners using 27 different protocols in order to validate the software. Comparative results correlating the software output and corresponding data previously obtained by the current quality control program routine were used to conduct this validation. For this comparison, two statistical tests were employed: the Students t-test (for slice thickness, slice increment, pixel size, and the coefficients of the CT number linearity evaluation, with a chosen p-value of 0.01) and the Fisher F-test (for the noise, with chosen p-value of 0.05).The functions MTF and NPS are not currently measured by the quality control routine, so there was no previous result for comparison. Instead, the NPS was fitted as a function of the MTF (using the theoretical relationship between both functions) and the quality of the fit was evaluated using the reduced chi-square. From 101 t values and 25 F values calculated, 2 and 1 were outside the acceptance interval, respectively. This result agrees with the chosen p-values, and therefore the software results are in good agreement with the traditional quality control routine results. The fits of NPS and MTF presented large uncertainties in the fitting parameters (uncertainties of the same order of magnitude as the parameters themselves). However, the reduced chi-square evaluation indicates a good fit (with the exception of one fit, which showed an anomaly on the measured NPS and was unconsidered). Therefore, the obtained MTF and NPS were in agreement with the theoretical expectations.

Radiotherapy planning involves the calculation of dose deposition throughout the patient, based upon quantitative electron density images from computed tomography (CT) scans taken before treatment. Cone beam CT (CBCT), consisting of a point source and flat panel detector, is often built onto radiotherapy delivery machines and used during a treatment session to ensure alignment of the patient to the plan. If the plan could be recalculated throughout the course of treatment, then margins of uncertainty and toxicity to healthy tissues could be reduced. CBCT reconstructions are normally too poor to be used as the basis of planning however, due to their insufficient sampling, beam hardening and high level of scatter. In this work, we investigate reconstruction techniques to enable dose calculation from CBCT. Firstly, we develop an iterative method for directly inferring electron density from the raw X-ray measurements, which is robust to both low doses and polyenergetic artefacts from hard bone and metallic implants. Secondly, we supplement this with a fast integrated scatter model, also able to take into account the polyenergetic nature of the diagnostic X-ray source. Finally, we demonstrate the ability to provide accurate dose calculation using our methodology from numerical and physical experiments. Not only does this unlock the capability to perform CBCT radiotherapy planning, offering more targeted and less toxic treatment, but the developed techniques are also applicable and beneficial for many other CT applications.