<p>The medical imaging system Sectra PACS from Sectra Imtec contains a 3D mode that can be used for visualising image stacks from e.g. computed tomography. Various structures of human anatomy can be visualised in the 3D mode, but visualisations of the bronchial tree of the lungs rarely become good enough to be useful. The goal of this work was to investigate ways of improving such visualisations.</p><p>Various approaches were studied, evaluated and tested. The fact that most effort was needed for small structures with sizes similar to the resolution of the images made things slightly more complicated. A method classifying neighbourhoods based on local structure emerged as most promising, and was used as foundation for a proposed algorithm. It creates a mask representing the presence of bronchi, allowing the hiding of uninteresting structures in its proximity. The algorithm was then implemented so that it could be tested together with the existing system.</p><p>The method was found to work well and was able to detect the smaller tubes of the bronchial tree and output the desired classification mask. Its usefulness was somewhat reduced by issues relating to speed, and the fact that many computed tomography image stacks lack the necessary resolution for visualising the finer details of the bronchial tree.</p>

Objective : To determine the relationship of tongue volume as determined from Cone Beam Computed Tomography (CBCT) scan reconstructions with maxillary and mandibular arch width, axial cross-sectional palatal perimeter, palatal index and axial inclination of upper and lower first premolars and molars. Method: Thirty subjects without prior orthodontic treatment swished barium sulfate to coat the tongue prior to CBCT imaging. The scan reconstructions were analyzed with three after-market softwares and intra-examiner reliability was assessed. Results: Absolute agreement intra-class correlation coefficients were used to determine reliability of the measurements. Pearson correlation coefficients and regression analysis were used to determine relationships. Conclusions: Tongue volume was strongly correlated with upper inter-molar width and palatal perimeter at the molar level, and least correlated with lower inter-molar width and axial inclination of the upper and lower first premolars and molars. The differences in measurements obtained from the three softwares were not statistically significant.

This thesis aims at introducing a methodology for clinical evaluation of orthodontic treatments using three-dimensional dento-maxillofacial images. Since complementary information is achieved by integrating multiple modalities, cone-beam computed tomography (CBCT) and stereophotogrammetry technologies are used to develop a methodology for tracking bone and facial skin variations over time. Our proposed methodology consists of a two-phase registration procedure. In the first phase, the multimodal images are registered using an extrinsic landmark-based registration followed by a robust Iterative Closest Points (ICP) method. In the second phase, by utilizing specific anatomical landmarks, single modal images of the skull and the mandible are registered over time using an intrinsic landmark-based registration method followed by the robust ICP algorithm. The results of registrations show that the signed error distribution of both mandible and skull registrations follow a normal distribution while all the errors fall within the CBCT precision range.

Larger and stronger muscles are positively associated with bone strength in the growing skeleton; however, less is known about the role of muscle properties on bone strength later in life. The primary objective of this study was to examine the relationship between muscle cross sectional area (MCSA), muscle force and rate of torque development (RTD) with bone strength indices (bone strength index (BSI) and strength strain index (SSI)) in the radius of healthy middle-aged adults. All bone and muscle measurements were determined in the non-dominant forearm in a sample of 40 healthy adults (23 men, 17 women: mean age 49.5, SD 2.3 yrs). Peripheral quantitative computer tomography (pQCT) was used to scan the distal and shaft sites of the radius bone in the forearm. MCSA was determined from the forearm shaft scan. Forearm muscle force was measured by hand grip dynamometry and RTD was obtained from isometric wrist flexion from an isokinetic dynamometry protocol. Hierarchical regression analyses were used to identify whether muscle properties (MCSA, grip force, and RTD) independently predicted radius bone strength indices (BSI and SSI), after adjusting for the confounders of sex, height and weight. Steps of the regression models that included sex, height, weight and a muscle property explained between 66% and 71% of variance in distal radius BSI and between 74% and 78% variance of estimated bone strength (SSI) at the shaft site (all steps p<0.001). MCSA explained a significant amount of variance in BSI (R2=0.08; p<0.01) and SSI (R2=0.04; p<0.05) at the radius. Grip force was also a significant predictor of SSI (R2=0.05; p<0.01) but not distal radius BSI (R2=0.03; p=0.07). Conversely, RTD explained a significant amount of variance in bone strength at the distal radius (R2=0.04; p<0.05), but not at the shaft (R2=0.01; p=0.17). These cross sectional findings support the theory that regional muscle size, force, and rate of torque development are related to estimated bone strength in the forearm at midlife. Further research should focus on targeted interventions to help determine which muscle property elicits a greater osteogenic response to optimize bone strength at distal and shaft sites of the radius.

Dual Energy Computed Tomography (DECT) is an emerging technique that offers new possibilities to determine composition of tissues in clinical applications. Accurate knowledge of tissue composition is important for instance for brachytherapy (BT) treatment planning. However, the accuracy of CT numbers measured with contemporary clinical CT scanners is relatively low since CT numbers are affected by image artifacts. The aim of this work was to estimate the accuracy of CT numbers measured with the Siemens SOMATOM Definition Flash DECT scanner and the accuracy of the resulting volume or mass fractions calculated via the three material decomposition method. CT numbers of water, gelatin and a 3rd component (salt, hydroxyapatite or protein powder) mixtures were measured using Siemens SOMATOM Definition Flash DECT scanner. The accuracy of CT numbers was determined by (i) a comparison with theoretical (true) values and (ii) using different measurement conditions (configurations) and assessing the resulting variations in CT numbers. The accuracy of mass fractions determined via the three material decomposition method was estimated by a comparison with mass fractions measured with calibrated scales. The latter method was assumed to provide highly accurate results. It was found that (i) axial scanning biased CT numbers for some detector rows. (ii) large volume of air surrounding the measured region shifted CT numbers compared to a configuration where the region was surrounded by water. (iii) highly attenuating object shifted CT numbers of surrounding voxels. (iv) some image kernels caused overshooting and undershooting of CT numbers close to edges. The three material decomposition method produced mass fractions differing from true values by 8% and 15% for the salt and hydroxyapatite mixtures respectively. In this case, the analyzed CT numbers were averaged over a volumetric region. For individual voxels, the volume fractions were affected by statistical noise. The method failed when statistical noise was high or CT numbers of the decomposition triplet were similar. Contemporary clinical DECT scanners produced image artifacts that strongly affected the accuracy of the three material decomposition method; the Siemens’ image reconstruction algorithm is not well suited for quantitative CT. The three material decomposition method worked relatively well for averages of CT numbers taken from volumetric regions as these averages lowered statistical noise in the analyzed data.

Human exposure to reduced weightbearing results in bone loss. The rate of bone loss during microgravity exposure is similar to that of a post-menopausal women. In fact, the maintenance of bone mass is intimately dependent on exercise. Therefore, exercise associated mechanical loads to bone tissue are an important countermeasure to prevent disuse-induced bone loss. However, the types of exercise modalities required to prevent such bone loss are unclear. Moreover, how mechanical loading to bone translates into molecular osteogenic signals in bone cells is unknown. Radiation exposure is another potent inducer of bone loss, namely observed on Earth in the clinical setting following radiotherapy procedures. It is expected that long duration space missions outside the protection of Earth’s magnetosphere will result in significant galactic cosmic radiation exposure. However, the magnitude of bone loss resulting from this galactic cosmic radiation exposure is unclear. Moreover, it is unknown if radiation exposure will exacerbate disuse-induced bone loss. Therefore, a series of experiments were designed to determine: 1) Will simulated galactic cosmic radiation exacerbate reduced weightbearing-induced bone loss? 2) Will pharmacological activation of the putative mechanosensing Wnt pathway enhance exercise-induced bone mass gain? To address these questions the experimental study series employed two animal models of reduced weightbearing, hindlimb unloading and partial weightbearing. These model test-beds enabled the evaluation of two novel countermeasures (simulated resistance exercise and glycogen synthase kinase-3 (GSK-3) therapeutic) and simulated exposure to space radiation environments. To test the impact of simulated space radiation (28Si) one study of the series was conducted at Brookhaven National Laboratory. To quantify the impact of the abovementioned countermeasures and space radiation on bone, mechanical testing, peripheral quantitative computed tomography, micro-computed tomography, histomorphometry, and immunohistochemistry served as primary outcome measures. The primary findings are: 1) Low-dose high-LET radiation negativity impacts maintenance of bone mass by lowering bone formation and increasing bone resorption. This impaired bone formation response is in part due to sclerostin induced suppression of Wnt signaling. 2) Combining GSK-3 inhibition with high intensity exercise mitigates cancellous bone loss and restores cortical periosteal growth during disuse.

Iterative CT reconstruction algorithms are superior to the standard convolution backpropagation (CBP) methods when reconstructing from a small number of views (hence less radiation), but are computationally costly. To reduce the execution time, this work implements and tests a parallel approach to iterative algorithms using a cluster of workstations, which is a low cost system found in many offices and non-academic sites. A previous implementation showed little speedup because of the significant cost of inter-processor communication. In this thesis, several data partitioning methods are examined, including some image tiling methods that exploit the spatial locality demonstrated by local CT. Using these methods, computation can proceed locally, without the need for inter-processor communication during every iteration. A relative speedup of up to 17 times is obtained using 25 processors, demonstrating that good performance can be obtained running computationally intensive CT reconstruction algorithms on distributed memory hardware. / October 2007

The medical imaging system Sectra PACS from Sectra Imtec contains a 3D mode that can be used for visualising image stacks from e.g. computed tomography. Various structures of human anatomy can be visualised in the 3D mode, but visualisations of the bronchial tree of the lungs rarely become good enough to be useful. The goal of this work was to investigate ways of improving such visualisations. Various approaches were studied, evaluated and tested. The fact that most effort was needed for small structures with sizes similar to the resolution of the images made things slightly more complicated. A method classifying neighbourhoods based on local structure emerged as most promising, and was used as foundation for a proposed algorithm. It creates a mask representing the presence of bronchi, allowing the hiding of uninteresting structures in its proximity. The algorithm was then implemented so that it could be tested together with the existing system. The method was found to work well and was able to detect the smaller tubes of the bronchial tree and output the desired classification mask. Its usefulness was somewhat reduced by issues relating to speed, and the fact that many computed tomography image stacks lack the necessary resolution for visualising the finer details of the bronchial tree.

Larger and stronger muscles are positively associated with bone strength in the growing skeleton; however, less is known about the role of muscle properties on bone strength later in life. The primary objective of this study was to examine the relationship between muscle cross sectional area (MCSA), muscle force and rate of torque development (RTD) with bone strength indices (bone strength index (BSI) and strength strain index (SSI)) in the radius of healthy middle-aged adults. All bone and muscle measurements were determined in the non-dominant forearm in a sample of 40 healthy adults (23 men, 17 women: mean age 49.5, SD 2.3 yrs). Peripheral quantitative computer tomography (pQCT) was used to scan the distal and shaft sites of the radius bone in the forearm. MCSA was determined from the forearm shaft scan. Forearm muscle force was measured by hand grip dynamometry and RTD was obtained from isometric wrist flexion from an isokinetic dynamometry protocol. Hierarchical regression analyses were used to identify whether muscle properties (MCSA, grip force, and RTD) independently predicted radius bone strength indices (BSI and SSI), after adjusting for the confounders of sex, height and weight. Steps of the regression models that included sex, height, weight and a muscle property explained between 66% and 71% of variance in distal radius BSI and between 74% and 78% variance of estimated bone strength (SSI) at the shaft site (all steps p<0.001). MCSA explained a significant amount of variance in BSI (R2=0.08; p<0.01) and SSI (R2=0.04; p<0.05) at the radius. Grip force was also a significant predictor of SSI (R2=0.05; p<0.01) but not distal radius BSI (R2=0.03; p=0.07). Conversely, RTD explained a significant amount of variance in bone strength at the distal radius (R2=0.04; p<0.05), but not at the shaft (R2=0.01; p=0.17). These cross sectional findings support the theory that regional muscle size, force, and rate of torque development are related to estimated bone strength in the forearm at midlife. Further research should focus on targeted interventions to help determine which muscle property elicits a greater osteogenic response to optimize bone strength at distal and shaft sites of the radius.

Neutron stimulated emission computed tomography (NSECT) is being proposed as an experimental technique to diagnose iron overload in patients. Proof-of-concept experiments have suggested that NSECT may have potential to make a non-invasive diagnosis of iron overload in a clinical system. The technique's sensitivity to high concentrations of iron combined with tomographic acquisition ability gives it a unique advantage over other competing modalities. While early experiments have demonstrated the efficacy of detecting samples with high concentrations of iron, a tomography application for patient diagnosis has never been tested. As with any other tomography system, the performance of NSECT will depend greatly on the acquisition parameters that are used to scan the patient. In order to determine the best acquisition geometry for a clinical system, it is important to evaluate and understand the effects of varying each individual acquisition parameter on the accuracy of the reconstructed image. This research work proposes to use Monte-Carlo simulations to optimize a clinical NSECT system for iron overload diagnosis.Simulations of two NSECT systems have been designed in GEANT4, a spectroscopy system to detect uniform concentrations of iron in the liver, and a tomography system to detect non-uniform iron overload. Each system has been used to scan simulated samples of both disease models in humans to determine the best scanning strategy for each. The optimal scanning strategy is defined as the combination of parameters that provides maximum accuracy with minimum radiation dose. Evaluation of accuracy is performed through ROC analysis of the reconstructed spectrums and images. For the spectroscopy system, the optimal acquisition geometry is defined in terms of the number of neutrons required to detect a clinically relevant concentration of iron. For the tomography system, the optimal scanning strategy is defined in terms of the number of neutrons and the number of spatial and angular translation steps used during acquisition. Patient dose for each simulated system is calculated by measuring the energy deposited by the neutron beam in the liver and surrounding body tissue. Simulation results indicate that both scanning systems can detect wet iron concentrations of 5 mg/g or higher. Spectroscopic scanning with sufficient accuracy is possible with 1 million neutrons per scan, corresponding to a patient dose of 0.02 mSv. Tomographic scanning requires 8 angles that sample the image matrix at 1 cm projection intervals with 4 million neutrons per projection, which corresponds to a total body dose of 0.56 mSv. The research performed for this dissertation has two important outcomes. First, it demonstrates that NSECT has the clinical potential for iron overload diagnosis in patients. Second, it provides a validated simulation of the NSECT system which can be used to guide future development and experimental implementation of the technique. / Dissertation