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Deep Learning Frameworks For Accelerated Magnetic Resonance Image Reconstruction Without Ground Truths, Ibsa Kumara Jalata

Graduate Theses and Dissertations

Magnetic Resonance Imaging (MRI) is typically a slow process because of its sequential data acquisition. To speed up this process, MR acquisition is often accelerated by undersampling k-space signals and solving an ill-posed problem through a constrained optimization process. Image reconstruction from under-sampled data is posed as an inverse problem in traditional model-based learning paradigms. While traditional methods use image priors as constraints, modern deep learning methods use supervised learning with ground truth images to learn image features and priors. However, in some cases, ground truth images are not available, making supervised learning impractical. Recent data-centric learning frameworks such as …

Temperature Mapping Using Mid-Field Magnetic Resonance Imaging, Diego F. Martinez

Electronic Thesis and Dissertation Repository

Magnetic Resonance Imaging (MRI) is a non-invasive imaging modality with excellent soft tissue contrast and sensitivity to tissue temperature. MRI use is growing in Canada with expectation that this is expected to continue in the medium term, with more wide adoption of MRI and in particular a renewed focus on MR systems which deviate from the most commonly used 1.5T field strength system. By implementing systems which do not use as strong magnets and instead operate

Generally, as the field strength of an MR system decreases, the signal received when imaging also decreases, which makes it difficult to implement some …

Neural Correlates Of Post-Traumatic Brain Injury (Tbi) Attention Deficits In Children, Meng Cao

Dissertations

Traumatic brain injury (TBI) in children is a major public health concern worldwide. Attention deficits are among the most common neurocognitive and behavioral consequences in children post-TBI which have significant negative impacts on their educational and social outcomes and compromise the quality of their lives. However, there is a paucity of evidence to guide the optimal treatment strategies of attention deficit related symptoms in children post-TBI due to the lack of understanding regarding its neurobiological substrate. Thus, it is critical to understand the neural mechanisms associated with TBI-induced attention deficits in children so that more refined and tailored strategies can …

Advancements In Magnetic Resonance Image Guided Radiotherapy, Austen Curcuru

McKelvey School of Engineering Theses & Dissertations

Magnetic resonance image guided radiation therapy (MRgRT) devices are a recently developed technology that integrate the excellent soft tissue contrast and real-time imaging capabilities of MRI with a medical linear accelerator (Linac). This provides an unprecedented ability to guide and adapt radiation therapy treatments based on real-time cine imaging. However, the merging of these technologies has come with unique challenges. MRI lacks the geometric fidelity of computed tomography (CT). Spatial inaccuracies in MRI can result from magnetic field (B0) or center frequency variations, gradient-induced eddy currents, and magnetic field gradient imperfections (e.g., nonlinearities, poor calibration, concomitant fields, and unsatisfactory electronic …

In Vivo Multi-Modal Imaging Approaches For Cancer, Stem And Immune Cells, Nourhan Shalaby

Electronic Thesis and Dissertation Repository

Introduction: Molecular imaging allows for non-invasive longitudinal visualization of cellular functions in vivo. This area of research has provided better understanding of fundamental molecular and biochemical processes, enabled optimization of pre-clinical and clinical assessments for new treatments, and allowed for more accurate and early detection of many pathologies. Extensive research for novel imaging techniques and emerging technologies have rapidly advanced the field. However, an ideal single imaging modality or approach does not exist. Alternatively, multi-modal imaging approaches are commonly applied to overcome limitations of individual technologies. In this thesis, we design, develop, validate, and image various cell types using …

Building A Magnetosome-Like Nanoparticle For Magnetic Resonance Imaging, Qin Sun

Electronic Thesis and Dissertation Repository

With its superb spatial and temporal resolution, magnetic resonance imaging (MRI) has great potential to track cellular activities that define early stages of disease. To improve molecular imaging techniques, we are developing MRI reporter gene expression based on the magnetosome. In magnetotactic bacteria (MTB), magnetosome formation compartmentalizes iron biominerals in membrane-enclosed vesicles. We hypothesize that essential magnetosome proteins interact in any cell type to form rudimentary magnetosome-like nanoparticles, providing a genetically-controlled contrast agent for molecular MRI.

MTB genes mamE, mamB, mamI, and mamL were cloned from M. magneticum sp. AMB-1 genomic DNA by PCR and inserted into …

Novel 129xe Magnetic Resonance Imaging And Spectroscopy Measurements Of Pulmonary Gas-Exchange, Alexander M. Matheson

Electronic Thesis and Dissertation Repository

Gas-exchange is the primary function of the lungs and involves removing carbon dioxide from the body and exchanging it within the alveoli for inhaled oxygen. Several different pulmonary, cardiac and cardiovascular abnormalities have negative effects on pulmonary gas-exchange. Unfortunately, clinical tests do not always pinpoint the problem; sensitive and specific measurements are needed to probe the individual components participating in gas-exchange for a better understanding of pathophysiology, disease progression and response to therapy.

In vivo Xenon-129 gas-exchange magnetic resonance imaging (¹²⁹Xe gas-exchange MRI) has the potential to overcome these challenges. When participants inhale hyperpolarized ¹²⁹Xe gas, it …

Investigating Applications Of Deep Learning For Diagnosis Of Post Traumatic Elbow Disease, Hugh James

McKelvey School of Engineering Theses & Dissertations

Traumatic events such as dislocation, breaks, and arthritis of musculoskeletal joints can cause the development of post-traumatic joint contracture (PTJC). Clinically, noninvasive techniques such as Magnetic Resonance Imaging (MRI) scans are used to analyze the disease. Such procedures require a patient to sit sedentary for long periods of time and can be expensive as well. Additionally, years of practice and experience are required for clinicians to accurately recognize the diseased anterior capsule region and make an accurate diagnosis. Manual tracing of the anterior capsule is done to help with diagnosis but is subjective and timely. As a result, there is …

Magnetic Resonance Systems Development For Point-Of-Care Mri Platforms, Eric J. Lessard

Electronic Thesis and Dissertation Repository

Magnetic resonance imaging utilizes electromagnets to produce anatomical images in both clinical and research settings. In the race towards increasing performance head-optimized scanners have begun playing a significant role in providing high quality imaging of the head. However, they are implemented using smaller geometries and as such fail to allow entrance of the patient past their shoulders. This is overcome by designing asymmetric gradient coils which have their imaging region located towards one end of the gradient coil, as opposed to the geometric center, allowing brain imaging. There exists interest in compact configurations which allow imaging further into the cervical …

Radiomic Features To Predict Overall Survival Time For Patients With Glioblastoma Brain Tumors Based On Machine Learning And Deep Learning Methods, Lina Chato

UNLV Theses, Dissertations, Professional Papers, and Capstones

Machine Learning (ML) methods including Deep Learning (DL) Methods have been employed in the medical field to improve diagnosis process and patient’s prognosis outcomes. Glioblastoma multiforme is an extremely aggressive Glioma brain tumor that has a poor survival rate. Understanding the behavior of the Glioblastoma brain tumor is still uncertain and some factors are still unrecognized. In fact, the tumor behavior is important to decide a proper treatment plan and to improve a patient’s health. The aim of this dissertation is to develop a Computer-Aided-Diagnosis system (CADiag) based on ML/DL methods to automatically estimate the Overall Survival Time (OST) for …

Fast Magnetic Resonance Image Reconstruction With Deep Learning Using An Efficientnet Encoder, Tahsin Rahman

Open Access Theses & Dissertations

This thesis aims to develop an efficient, deep network based method for Magnetic Resonance Imaging (MRI) acceleration through undersampled MR image reconstruction. Deep Neural Networks, particularly Deep Convolutional Networks, have been demonstrated to be highly effective in a wide variety of computer vision tasks, including MRI reconstruction. However, modern highly efficient encoder structures, such as the EfficientNet can potentially reduce reconstruction times further while improving reconstruction quality. To that end, we have developed a multi-channel U-Net MRI reconstruction network which uses an EfficientNet encoder and a custom asymmetric. The network was trained and tested using 5x undersampled multi-channel brain MR …

Measuring Inflammation In The Entire Myocardium In A Canine Model Of Myocardial Infarction With Hybrid Pet/Mri, Benjamin Wilk

Electronic Thesis and Dissertation Repository

Background: After myocardial infarction (MI), fibrosis and an ongoing dysregulated inflammatory response are associated with adverse cardiac remodeling. Fluorodeoxyglucose (FDG) positron emission tomography (PET) is sensitive to inflammation provided suppression protocols are implemented to restrict the uptake of glucose in myocytes. Magnetic resonance imaging can be used to determine extracellular volume, a surrogate measure of fibrosis. In some cases, patients present with markedly reduced flow in the setting of a large infarct, i.e. microvascular obstruction, restricting the delivery of FDG and contrast agents. To overcome this problem, a constant infusion was explored as an alternative to the clinical standard bolus …

Validity Of Intrinsic Foot Muscle Size Measured By Ultrasound And Mri, Dallin Swanson

Undergraduate Honors Theses

Intrinsic foot muscles maintain foot structural integrity and contribute to functional movement, posture and balance. Thus, assessing intrinsic foot muscle size and strength are important. Magnetic resonance imaging (MRI) has been shown to accurately image the individual muscles but is costly and time consuming. Ultrasound (US) imaging may provide an alternative that is less costly and more readily available. The purpose of this study was to investigate the validity and reproducibility of US imaging in measuring intrinsic foot muscle size in comparison to MRI. US and MRI were employed to measure the intrinsic foot muscle size involving 35 participants (females …

Ischemic Stroke Thrombus Characterization Through Quantitative Magnetic Resonance Imaging, Spencer D. Christiansen

Electronic Thesis and Dissertation Repository

Stroke is a pervasive, devastating disease and remains one of the most challenging conditions to treat. In particular, risk of recurrence is dramatically heightened after a primary stroke and requires urgent preventative therapy to effectively mitigate. However, the appropriate preventative therapy depends on the underlying source of the stroke, known as etiology, which is challenging to determine promptly. Current diagnostic tests for determining etiology underwhelm in both sensitivity and specificity, and in as much as 35% of cases etiology is never determined. In ischemic stroke, the composition of the occluding thrombus, specifically its red blood cell (RBC) content, has been …

Assessing Midbrain Abnormalities In Parkinson’S Disease Using Magnetic Resonance Imaging, Kiarash Ghassaban

Wayne State University Dissertations

Diagnosing early-stage Parkinson’s disease (PD) and its manifestations is still a clinical challenge. Previous imaging studies using iron, neuromelanin (NM) and the Nigrosome-1 (N1) measures in the substantia nigra (SN) by themselves have been unable to provide sufficiently high diagnostic performance for these methods to be adopted clinically. In this dissertation, we start by studying idiopathic PD patients at their intermediate stages of the disease to evaluate the role of global and regional iron in the major deep gray matter nuclei. Then, we only focus on the NM complex in the midbrain and how neuronal loss interact with iron overload …

The Theory And Design Of Class E Power Amplifiers For Impulse Excitation In Nuclear Magnetic Resonance, Owen D. Riemer

Browse all Theses and Dissertations

A new method for analyzing the effectiveness of NMR impulse power amplifiers was developed using a classical linear systems approach to NMR. The method demonstrates a way to compare NMR power amplifiers and outputs. Thermodynamic calculations and the harmonic content of NMR amplifiers is presented to provide a complete description of the NMR power amplifier design problem. A design procedure for class E NMR power amplifiers with a pi-impedance matching network is outlined for matching the amplifier to the transmitter coil. The thesis concludes with the presentation of a 53 MHz power amplifier developed with the procedure. The complete amplifier …

Comparing Neuromuscular System Function In Healthy And Mobility-Impaired Older Females, Neal B. Mckinnon

Electronic Thesis and Dissertation Repository

Objectives: The objective of this thesis was to evaluate and compare neuromuscular system function in a group of young, healthy old and mobility-impaired older females (gait speed less than 1m/s) in an attempt to identify which neuromuscular factors contribute most to the loss of mobility and functional performance with age.

Methods: The ankle dorsiflexor and knee extensor muscles were used as a model in these studies. First, in Chapter 2 quantitative electromyography (EMG) was used to evaluate motor unit (MU) numbers, properties and the fidelity of the neuromuscular junction. Next, Chapter 3 conducted magnetic resonance imaging (MRI) to examine contractile …

Hyperpolarized Carbon-13 Magnetic Resonance Measurements Of Tissue Perfusion And Metabolism, Keith Michel

Dissertations & Theses (Open Access)

Hyperpolarized Magnetic Resonance Imaging (HP MRI) is an emerging modality that enables non-invasive interrogation of cells and tissues with unprecedented biochemical detail. This technology provides rapid imaging measurements of the activity of a small quantity of molecules with a strongly polarized nuclear magnetic moment. This polarization is created in a polarizer separate from the imaging magnet, and decays continuously towards a non-detectable thermal equilibrium once the imaging agent is removed from the polarizer and administered by intravenous injection. Specialized imaging strategies are therefore needed to extract as much information as possible from the HP signal during its limited lifetime.

In …

Computational Unfolding Of The Human Hippocampus, Jordan M. K. Dekraker

Electronic Thesis and Dissertation Repository

The hippocampal subfields are defined by their unique cytoarchitectures, which many recent studies have tried to map to human in-vivo MRI because of their promise to further our understanding of hippocampal function, or its dysfunction in disease. However, recent anatomical literature has highlighted broad inter-individual variability in hippocampal morphology and subfield locations, much of which can be attributed to different folding configurations within hippocampal (or archicortical) tissue. Inspired in part by analogous surface-based neocortical analysis methods, the current thesis aimed to develop a standardized coordinate framework, or surface-based method, that respects the topology of all hippocampal folding configurations. I developed …

Quantification Of White Matter Hyperintensities In Long-Term Survivors Of Childhood Brain Tumor: Relationships With Cognition, Holly A. Aleksonis

Psychology Theses

This study investigated relationships among quantified white matter hyperintensity (WMH) volumes and core cognitive skills in long-term survivors of childhood posterior fossa tumor utilizing a novel automated neuroimaging approach. Thirty-five survivors and 56 healthy controls underwent MRI and neuropsychological testing. Results indicated that log transformed normalized total WMH volumes differentiated groups based on treatment type, where survivors treated with chemoradiation therapy had significantly higher volumes of total WMH compared to survivors with surgery only and healthy controls, and survivors with surgery only had higher WMH volumes than healthy controls. In the total sample, higher total WMH volumes were associated with …

Investigating The Metabolic Progression Of Glioblastoma With Hyperpolarized Magnetic Resonance, Travis Salzillo

Dissertations & Theses (Open Access)

Rapid diagnosis and therapeutic monitoring of aggressive diseases such as glioblastoma (GBM) can improve patient survival by providing physicians the time to optimally deliver treatment. This includes early in development, while the tumor is still manageable, or following initial therapy, when alternative treatments should be considered. The main goal of this project was to determine whether metabolic imaging with hyperpolarized magnetic resonance spectroscopy (MRS) could detect changes in tumor progression more rapidly than conventional anatomic magnetic resonance imaging (MRI) in patient-derived GBM murine models. To comprehensively capture the dynamic nature of cancer metabolism, in vivo pyruvate-to-lactate conversion with hyperpolarized MRI, …

Pulmonary Imaging Of Chronic Obstructive Pulmonary Disease Using Multi-Parametric Response Maps, Jonathan Macneil

Electronic Thesis and Dissertation Repository

Chronic obstructive pulmonary disease (COPD) is characterized by irreversible airflow obstruction caused by airway remodelling and parenchymal destruction. Clinically, observation of COPD is performed using spirometry, but this technique only provides a global measure of lung health. To supplement these clinical measurements, thoracic computed tomography (CT) and hyperpolarized gas magnetic resonance imaging (MRI) have been used to measure regional structure and function abnormalities. Although CT and MRI have been used to research COPD, combination of both modalities into an interrelated image has never been performed. Therefore, we developed an image processing pipeline to combine MRI-CT information into a multi-parametric response …

Assessment Of White Matter Hyperintensity, Cerebral Blood Flow, And Cerebral Oxygenation In Older Subjects Stratified By Cerebrovascular Risk, Ahmed A. Bahrani

Theses and Dissertations--Biomedical Engineering

Objective: Cerebrovascular disease (CVD) is the fifth most common cause of mortality in the United States. Diagnosis of CVD at an early stage is critical for optimal intervention designed to prevent ongoing and future brain injury. CVD is commonly associated with abnormalities of the cerebral microvasculature leading to tissue dysfunction, neuronal injury and death, and resultant clinical symptoms, which in turn, further impacts cerebral autoregulation (CA). This series of studies aims to test the hypothesis that white matter hyperintensities (WMH) and cerebral hemodynamics (quantified by magnetic resonance imaging (MRI) and an by innovative hybrid near-infrared diffuse optical instrument) can be …

Mid-Fusiform Sulcus Anatomy And Its Relationship To Face Processing And Social Functioning In Autism Spectrum Disorder, Carla Ammons

All ETDs from UAB

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by deficits in social communication and restricted and repetitive behaviors and interests. One of the most consistent findings in ASD is reduced attention to and atypical processing of faces. However, the brain basis of aberrant face processing in ASD remains opaque. A novel neuroanatomical feature, the mid-fusiform sulcus (MFS), is strongly associated with face-selective regions of the fusiform gyrus (FG) as well as other large-scale functional and structural divisions in the ventral temporal cortex (Weiner et al., 2014). However, this feature is unexplored in ASD. The overarching goal of this dissertation …

A Computational Method For The Analysis Of Magnetic Resonance Images Using Morphological Analysis, Jon Rolf Marstrander

All ETDs from UAB

Neurodegenerative diseases are an increasingly significant source of health problems in recent years. The prevalence and severity of these diseases is only expected to grow with the aging of the population. There is a large and and growing research effort to understand, diagnose and develop treatments for this class of diseases. Many of these diseases are not well understood, and there is a dearth of approved biomarkers and other techniques to definitively diagnose these diseases. The field of computational neuroimaging has been developed as part of the effort to study and diagnose these diseases. This field has undergone explosive growth …

The Effect Of Spatial Averaging On Db/Dt Exposure Values For Implanted Medical Devices, Christopher Ap Brown

Electronic Thesis and Dissertation Repository

Magnetic resonance imaging (MRI) is a medical imaging modality that has seen continuous growth in the decades since its introduction. In conjunction with this increase in the use of MRI, there has also been a growth in the number of patients having implanted medical devices, such as pacemakers. These devices can have undesirable interactions with the MR system. The safety of these interactions must be guaranteed while ensuring that safety limits are not so conservative that they would preclude too many patients from benefiting from MRI. One factor that could make limits less restrictive is spatial averaging of the fields …

Development Of A Computational Method For Assessing Static Field Induced Torque On Medical Implants, Xiao Fan Ding

Electronic Thesis and Dissertation Repository

The objective of this thesis is the development of a computational method for finding the torque induced on an object when placed in the static magnetic field of an MR scanner. As a preliminary step, the classic EM problems of a sphere and infinitely long cylinder of linear material was modeled in commercially available simulation software. Upon verification of the parameters implemented, the second step is the simulation of simple objects with realistic material properties, stainless-steel cylinders. Physical cylinders were machined to match those in the simulations and underwent the ASTM standard method for measuring induced torque. An adjacent study …

Texture Analysis And Machine Learning To Predict Pulmonary Ventilation From Thoracic Computed Tomography, Andrew Westcott

Electronic Thesis and Dissertation Repository

Chronic obstructive pulmonary disease (COPD) leads to persistent airflow limitation, causing a large burden to patients and the health care system. Thoracic CT provides an opportunity to observe the structural pathophysiology of COPD, whereas hyperpolarized gas MRI provides images of the consequential ventilation heterogeneity. However, hyperpolarized gas MRI is currently limited to research centres, due to the high cost of gas and polarization equipment. Therefore, I developed a pipeline using texture analysis and machine learning methods to create predicted ventilation maps based on non-contrast enhanced, single-volume thoracic CT. In a COPD cohort, predicted ventilation maps were qualitatively and quantitatively related …

Understanding The Contributions Of Alzheimer’S Disease & Cardiovascular Risks To Cerebral Small Vessel Disease Manifest As White Matter Hyperintensities On Magnetic Resonance Imaging (Mri), Omar M. Al-Janabi

Theses and Dissertations--Clinical and Translational Science

Introduction: Alzheimer’s Diseases (AD) & cerebral small vessel disease associated with cardiovascular risk factors (cSVD) frequently coexist, differentially affecting both imaging and clinical features associated with aging and dementia. We hypothesized that Magnetic Resonance Imaging (MRI) can be used in novel ways to identify relative contributions of AD & cardiovascular risks to cSVD and brain atrophy, generating new biomarkers & insights into mixed disease states associated with cognitive decline and dementia.

Methods: Three experiments were conducted to address the overarching hypothesis. First, we visually rated the clinical MRI of 325 participants from a community-based cross-sectional sample to elucidate the relative …

Calibrated Short Tr Recovery Mri For Rapid Measurement Of Brain-Blood Partition Coefficient And Correction Of Quantitative Cerebral Blood Flow, Scott William Thalman

Theses and Dissertations--Biomedical Engineering

The high prevalence and mortality of cerebrovascular disease has led to the development of several methods to measure cerebral blood flow (CBF) in vivo. One of these, arterial spin labeling (ASL), is a quantitative magnetic resonance imaging (MRI) technique with the advantage that it is completely non-invasive. The quantification of CBF using ASL requires correction for a tissue specific parameter called the brain-blood partition coefficient (BBPC). Despite regional and inter-subject variability in BBPC, the current recommended implementation of ASL uses a constant assumed value of 0.9 mL/g for all regions of the brain, all subjects, and even all species.

The …