Browsing by Subject "CT"
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Item Automated Determination of Arterial Input Function Areas in Perfusion Analysis(2013-04-04) Liu, QunPerfusion in biological system refers to capillary-level blood flow in tissues, and is a critical parameter used for detecting physiological changes. Medical imaging provides an effective way to measure tissue perfusion. Quantitative analysis of perfusion studies requires the accurate determination of the arterial input function (AIF), which describes the delivery of intravascular tracers to tissues. Automating the process of finding the AIF can save operating time, remove the inter-operator variability, and correct the errors in the presence of the dispersion of the arterial system. Even though several methods are currently developed for automatically extracting an AIF, they are specific to a single modality and particular to a certain tissue. In this thesis, we developed an algorithm to automatically determine an AIF by classifying the characteristic parameters of image pixels' dynamic evaluation curves between blood feeding areas and tissues. This automated AIF determination can be used to facilitate the generation of parametric maps for perfusion studies based on various imaging modalities and covering a variety of tissues. Automatic AIF determination was accomplished by extracting characteristic parameters such as maximum slope, maximum enhancement, time to peak, time to wash-out, and wash-out slope. Multi-dimensional data containing the characteristic parameters were converted and reduced into two-dimensional (2-D) representations, which were presented as a plurality of 2-D plots. Then physiological phases were localized within the simplified representations. Automated segmentation of non-AIF tissues and determination of AIF areas were accomplished by automatically finding peaks and valleys of each physiological phase on the plurality of 2-D plots. The algorithm was tested in CT myocardial perfusion studies, in which a pig was used as a model of myocardial ischemia and perfusion. PET gastrointestinal (GI) perfusion studies were performed using this algorithm, in which GI perfusion was evaluated when cardiac outputs were controlled with four modes. This automated AIF determination study was compared with manual selection of AIF in PET imaging and microsphere studies to assess the effectiveness of this algorithm. In the CT myocardial perfusion study, the perfusion of infarcted myocardium was significantly lower than that of non-infarcted areas and lower than that when it was normal. In the PET abdominal perfusion study, PET imaging data gives lower value of standard deviation relative to the mean than that in microsphere results. In the manual AIF selection study, a slight change in selecting the AIF region caused a big influence on the result. On the contrary, the automated AIF selection remains consistent in the entire study and reduces inter-operator variation. A conclusion was made that this technique is applicable to several imaging modalities, such as PET, CT and MRI, and is effective on many tissues. In addition, this algorithm is straightforward and provides consistent results. More importantly, this automated AIF determination technique replaces the conventional spatial classification method with the functional classification method, taking more physiological considerations and explanations involved.Item Constraining fracture permeability by characterizing fracture surface roughness(2010-12) Al-Johar, Mishal Mansour; Sharp, John Malcolm, 1944-; Ketcham, Richard A.; Cardenas, Meinhard B.Open and connected fractures, where present, control fluid flow and dominate solute transport. Flow through fractures has major implications for water resource management, underground waste repositories, contaminant remediation, and hydrocarbon exploitation. Complex fracture morphology makes it difficult to quantify and predict flow and transport accurately. The difficulty in usefully describing the complex morphology of a real fracture from a small 3-D volume or 2-D profile sample remains unresolved. Furthermore, even when complex fracture morphology is measured across three-dimensions, accurate prediction of discharge remains difficult. High resolution x-ray computed tomography (HXRCT) data collected for over 20 rock surfaces and fractures provide a useful dataset to study fracture morphology across scales of several orders of magnitude. Samples include fractured rock of varying lithology, including sandstone, volcanic tuffs and crystalline igneous and metamorphic rocks. Results suggest that the influence of grain size on surface roughness is not readily apparent due to other competing variables such as mechanics, skins and coatings, and weathering and erosion. Flow tests of HXRCT-scanned fractures provide real discharge data allowing the hydraulic aperture to be directly measured. Scale-invariant descriptions of surface roughness can produce constrained estimates of aperture variability and possibly yield better predictions of fluid flow through fractures. Often, a distinction is not made between the apparent and true fracture apertures for rough fractures measured on a 2-D topographic grid. I compare a variety of local aperture measurements, including the apparent aperture, two-dimensional circular tangential aperture, and three-dimensional spherical tangential aperture. The mechanical aperture, the arithmetic mean of the apparent local aperture, is always the largest aperture. The other aperture metrics vary in their ranking, but remain similar. Results suggest that it may not be necessary to differentiate between the apparent and true apertures. Rock fracture aperture is the predominant control on permeability, and surface roughness controls fracture aperture. A variety of surface roughness characterizations using statistical and fractal methods are compared. A combination of the root-mean-square roughness and the surface-to-footprint ratio are found to be the most useful descriptors of rock fracture roughness. Mated fracture surfaces are observed to have nearly identical characterizations of fracture surface roughness, suggesting that rock fractures can be sampled by using only one surface, resulting in a significantly easier sampling requirement. For mated fractures that have at least one point in contact, a maximum potential aperture can be constrained by reflecting and translating a single surface. The maximized aperture has a nearly perfect correlation with the RMS roughness of the surface. These results may allow better predictions of fracture permeability thereby providing a better understanding of subsurface fracture flow for applications to contaminant remediation and water and hydrocarbon management. Further research must address upscaling fracture morphology from hand samples to outcrops and characterizing entire fracture networks from samples of single fractures.Item Skeletal ontogeny of Monodelphis domestica (Mammalia: Didelphidae) : quantifying variation, variability, and technique bias in ossification sequence reconstruction(2013-12) Morris, Zachary Stephen; Rowe, Timothy, 1953-The field of evolutionary developmental biology (evo-devo) focuses on understanding the evolution of ontogeny and mechanisms of evolutionary change. Recently, taxonomic comparisons of the sequence of skeletal ossification have become prominent in evo-devo. However, most of these studies fail to consider two major issues: how the technique used to assay ossification and ontogenetic variation and variability may affect comparisons among taxa. This study focuses on the onset of ossification in the skeleton of Monodelphis domestica and quantifies the affects of variation, variability, and technique bias on reconstructions of ontogeny. Previous comparisons among mammalian taxa have used both computed tomography (CT) and clearing-and-staining (CS) to assess the presence or absence of skeletal elements (i.e., skeletal maturity). In this study, CT and CS were used on the same specimen to compare how these methods assess skeletal maturity. The comparisons of the same individual under reveal significant differences in how skeletal maturity is assessed by CT and CS techniques. Further, significant biases were recovered between techniques. CT is more likely to reveal cranial elements that CS does not, whereas CS is more likely to reveal appendicular elements that CT does not. To assess levels of variation and variability, Ontogenetic Sequence Analysis (OSA) was used to characterize the ontogeny of Monodelphis domestica. This revealed significant levels of variation with over 800 different ontogenetic pathways recovered for the onset of ossification of all skeletal elements studied. Additionally, high levels of variability were also reconstructed because the majority of specimens were found to exhibit non-modal ontogenetic sequences. This variability is more highly concentrated in the sequence of cranial ossification, suggesting potential modularity in ontogenetic variation and variability. Finally, OSA revealed that technique bias could importantly affect reconstructions of skeletal ossification sequences because no identical sequences were recovered by the CT and CS datasets. The results of this study demonstrate the importance of considering the primary nature of developmental studies, the specimen. Only by recognizing and quantifying the complexities of evo-devo research, especially natural variation and methodological biases, can more complete understandings of the evolution of ontogeny be had.Item Using Advanced Imaging to Study Fish(2013-05-31) Browning, Zoe SwezyAlthough mammals are the most commonly utilized laboratory animal, laboratory animal medicine continually seeks to replace them with animals of lower phylogenic classification. Fish are becoming increasingly important as investigators seek alternative animal models for research. Fish can provide an economical and feasible alternative to typical mammalian models; moreover, many fish, which have comparatively short life spans, can easily reproduce in the laboratory. One key area of animal health research in which fish have been underutilized is the field of advanced imaging. Although many images of fish have been captured through the use of computed tomography (CT), radiography, and ultrasonography, these images have been primarily utilized for anatomical study. In addition, fish have never before been studied with positron emission tomography/ computed tomography (PET/CT). My objectives were to determine if these imaging techniques can be used to obtain physiological information from fish, therefore making it more likely that fish can be utilized as replacement animals using these new imaging techniques (CT, PET/CT). I performed two different types of studies to assess the potential application of advanced imaging techniques to fish. In the first experiment, microCT was used to characterize otolith deformity in vitamin C deficient captive-raised red drum and relate the deformity to behavioral and physiological changes. I found that the normal and abnormal fish had statistically significant differences in behavior, cortisol levels, and otolith volume and density. MicroCT assessment of abnormal fish revealed operculum abnormalities, malocclusions, and several types of otolith malformations. Therefore, the affected fish had not only an abnormal skeletal appearance but also significantly abnormal behavior and cortisol responses. In the second experiment, fluorodeoxyglucose-positron emission tomography/ computed tomography (FDG-PET/CT) was used to quantify glucose uptake in select organs prior to carcinogenesis studies in fish. The quantified glucose uptake was compared to published data on humans, mice, and dogs. Rapid, quantifiable glucose uptake was demonstrated, particularly in brain, kidneys, and liver in all imaged fish species. Glucose uptake in the major organ systems of fish was closer to that in humans than uptake in mice or dogs, indicating that fish may serve as an effective alternative animal model for tumor studies using this technology. Other applications for this technique in fish may include metabolism studies and screening for environmental carcinogenesis. I found that both microCT and PET/CT imaging provided useful and meaningful results. In addition, the use of non-invasive scanning allows for re-use of fish, thus reducing the number of animal models used in experiments. These experiments suggest that fish will be good replacement models for mammals using these advanced imaging techniques.