Medicine and Health Sciences Commons^™

An Explainable Deep Learning Prediction Model For Severity Of Alzheimer's Disease From Brain Images, Godwin O. Ekuma

MSU Graduate Theses

Deep Convolutional Neural Networks (CNNs) have become the go-to method for medical imaging classification on various imaging modalities for binary and multiclass problems. Deep CNNs extract spatial features from image data hierarchically, with deeper layers learning more relevant features for the classification application. The effectiveness of deep learning models are hampered by limited data sets, skewed class distributions, and the undesirable "black box" of neural networks, which decreases their understandability and usability in precision medicine applications. This thesis addresses the challenge of building an explainable deep learning model for a clinical application: predicting the severity of Alzheimer's disease (AD). AD …

Automation Through Deep-Learning To Quantify Ventilation Defects In Lungs From High-Resolution Isotropic Hyperpolarized 129xe Magnetic Resonance Imaging, Tuneesh Kaur Ranota

Electronic Thesis and Dissertation Repository

Obstructive lung diseases are characterized by heterogenous ventilation. Hyperpolarized ¹²⁹Xe gas lung magnetic resonance imaging (MRI) can examine lung ventilation heterogeneity by acquiring high-resolution isotropic images. The current gold standard of semi-automated (SA) segmentation can be used to quantify non-isotropic ¹²⁹Xe lung images to generate ventilation defect percent (VDP), however, this method is not suitable for analysis of isotropic voxel ¹²⁹Xe images due to the large number of slices. Therefore, we used a fully automated deep learning-based (DL) lung algorithm to calculate VDP from isotropic images. SNR, SA and DL-based VDP were calculated, showing a strong positive …

Modeling Of Patient-Specific Periaortic Mechanics And Pulmonary Artery Hemodynamics Based On Phase-Contrast Magnetic Resonance Imaging Sequences., Johane H. Bracamonte

Theses and Dissertations

Inverse modeling in cardiovascular medicine is a collection of methodologies that can provide non-invasive patient-specific estimations of clinical risk factors using medical imaging as inputs. Its incorporation into clinical practice has the potential to improve diagnosis and treatment planning with low associated risks and costs.

Herein, three different phase contrast magnetic resonance imaging (MRI) modalities were implemented as input data, displacement encoding with stimulated echoes (DENSE MRI) applied, and time-resolved velocity encoding phase-contrast MRI, in 1D and 3D, applied to pulmonary artery (PA) hemodynamics.

A model to account for the effect of periaortic interactions due to static and dynamic structures …

Imaging Based Prediction Of Pathology In Adult Diffuse Glioma With Applications To Therapy And Prognosis, Evan Gates

Dissertations & Theses (Open Access)

The overall aggressiveness of a glioma is measured by histologic and molecular analysis of tissue samples. However, the well-known spatial heterogeneity in gliomas limits the ability for clinicians to use that information to make spatially specific treatment decisions. Magnetic resonance imaging (MRI) visualizes and assesses the tumor. But, the exact degree to which MRI correlates with the actual underlying tissue characteristics is not known.

In this work, we derive quantitative relationships between imaging and underlying pathology. These relations increase the value of MRI by allowing it to be a better surrogate for underlying pathology and they allow evaluation of the …

Does An Acute Achilles Tendon Rupture Become A Patient's Achilles Heel In The Long-Term?, Michaela Cm Khan

Electronic Thesis and Dissertation Repository

It is unknown if deficits in the involved limb following acute Achilles tendon rupture (AATR) persist in the long-term, or differ between patients treated operatively or non-operatively. This study investigated 43 patients 15±1 years post-AATR from a previous randomized controlled trial (RCT) that compared operative and non-operative treatment. Structural characteristics in the Achilles tendon and surrounding musculature were assessed using magnetic resonance imaging. We also performed physical examinations and evaluated performance-based and patient-reported outcomes. Overall, there were substantial differences between the involved and uninvolved limbs in most outcomes. Some outcomes improved over time from the initial RCT to the final …

Quantitatively Studying Tissue Damage In Multiple Sclerosis Using Gradient Recalled Echo Mri Sequences, Biao Xiang

Arts & Sciences Electronic Theses and Dissertations

Multiple Sclerosis (MS) is an unpredictable, often disabling disease of the central nervous system (CNS) that disrupts the flow of information within the brain, and between the brain the body. MS is the most common progressive neurologic disease of young adults, affecting approximately 2.3 million people worldwide. It is estimated that more than 700,000 individuals are affected by MS in United States. While MS has been studied for decades, the cause of it is still not definite and a fully effective treatment for MS is not yet available. Magnetic resonance imaging (MRI) has been used extensively in MS diagnosis and …

Investigating In Vivo Brain Metabolite Levels In Concussed Female Athletes And A Murine Model Of Repetitive Closed Head Injury, Amy L. Schranz

Electronic Thesis and Dissertation Repository

After a concussion there is a complex cascade of events, termed the neurometabolic cascade, that includes changes in ion flux, neurotransmission, and cellular energetics. How this pathophysiological process translates into cognitive deficits remains poorly understood. Magnetic resonance spectroscopy (MRS) provides a non-invasive technique that allows for the quantification of brain metabolites that are involved in these processes, including glutamate and glutamine, which are involved in neurotransmission. Moreover, female athletes are underrepresented in studies on concussion, limiting our knowledge and understanding of sex differences. The overall goal of this thesis was to examine metabolite changes using MRS in female athletes before …

Ultra-High Field Magnetic Resonance Imaging For Stereotactic Neurosurgery, Jonathan Lau

Electronic Thesis and Dissertation Repository

Stereotactic neurosurgery is a subspecialty within neurosurgery concerned with accurate targeting of brain structures. Deep brain stimulation (DBS) is a specific type of stereotaxy in which electrodes are implanted in deep brain structures. It has proven therapeutic efficacy in Parkinson’s disease and Essential Tremor, but with an expanding number of indications under evaluation including Alzheimer’s disease, depression, epilepsy, and obesity, many more Canadians with chronic health conditions may benefit. Accurate surgical targeting is crucial with millimeter deviations resulting in unwanted side effects including muscle contractions, or worse, vessel injury. Lack of adequate visualization of surgical targets with conventional lower field …

Retrospective Motion Correction In Magnetic Resonance Imaging Of The Brain, Patricia Johnson

Electronic Thesis and Dissertation Repository

Magnetic Resonance Imaging (MRI) is a tremendously useful diagnostic imaging modality that provides outstanding soft tissue contrast. However, subject motion is a significant unsolved problem; motion during image acquisition can cause blurring and distortions in the image, limiting its diagnostic utility. Current techniques for addressing head motion include optical tracking which can be impractical in clinical settings due to challenges associated with camera cross-calibration and marker fixation. Another category of techniques is MRI navigators, which use specially acquired MRI data to track the motion of the head.

This thesis presents two techniques for motion correction in MRI: the first is …

In Vivo Tracking Of Tumour Associated Macrophages In Breast Cancer With Magnetic Resonance Imaging, Ashley V. Makela

Electronic Thesis and Dissertation Repository

Introduction: The environment in which a tumour exists and functions is called the tumour microenvironment (TME). In breast cancer, the presence of tumour associated macrophages (TAMs) in the TME is associated with tumour aggressiveness and poor outcomes. Despite evidence for a link between TAM content and outcome, there are few strategies to measure TAMs and no in vivo approach. Iron or fluorine-19 (¹⁹F)-based MRI can be used to detect macrophages post intravenous injection of either an iron or perfluorocarbon (PFC) agent. Iron-based MRI is sensitive but difficult to quantify. ¹⁹F MRI is specific and signal is proportional …

Investigations Into The Effects Of Water Exchange And The Structure Of Lanthanide Chelates, Katherine Marie Payne

Dissertations and Theses

Lanthanide chelates are effective agents for improving contrast in MR images. Optimizing the relaxation of inner sphere water molecules is a common focus of research in this field. However, the efforts to design an optimal contrast agent have commonly over-looked the relationship of water position and water exchange kinetics. This work explores structural conformation, the impact of very fast water exchange kinetics on hydration, and differing tumbling rates for regioisomers of a number of lanthanide chelates. We have grown crystals of LnDOTMA and obtained structural data by X-ray diffraction that provide a picture of the chelate during water exchange and …

Development Of Anatomical And Functional Magnetic Resonance Imaging Measures Of Alzheimer Disease, Samaneh Kazemifar

Electronic Thesis and Dissertation Repository

Alzheimer disease is considered to be a progressive neurodegenerative condition, clinically characterized by cognitive dysfunction and memory impairments. Incorporating imaging biomarkers in the early diagnosis and monitoring of disease progression is increasingly important in the evaluation of novel treatments. The purpose of the work in this thesis was to develop and evaluate novel structural and functional biomarkers of disease to improve Alzheimer disease diagnosis and treatment monitoring. Our overarching hypothesis is that magnetic resonance imaging methods that sensitively measure brain structure and functional impairment have the potential to identify people with Alzheimer’s disease prior to the onset of cognitive decline. …

Mapping The Flip Angle In Magnetic Resonance Imaging Using The Accelerated 3d Look-Locker Sequence, Trevor P. Wade

Electronic Thesis and Dissertation Repository

In the ongoing quest to extract more information from MRI images, there has arisen a need to rapidly map the flip angle. This has been primarily driven by the shift to stronger main field strengths, which bring with them improved SNR, but also new difficulties. In particular, the radio frequency field used to excite the magnetization can no longer be assumed uniform at field strengths of 3 Tesla and above. New rapid quantitative imaging techniques, such as DESPOT1 and DESPOT2, rely on accurate knowledge of the flip angle, and while this could safely be assumed to be the prescribed value …

Effect Of Acute Administration Of Angiopoietin-1 In Experimental Traumatic Spinal Cord Injury: Magnetic Resonance Imaging And Neurobehavioral Studies, Chirag B. Patel

Dissertations & Theses (Open Access)

Spinal cord injury (SCI) is a devastating condition that affects people in the prime of their lives. A myriad of vascular events occur after SCI, each of which contributes to the evolving pathology. The primary trauma causes mechanical damage to blood vessels, resulting in hemorrhage. The blood-spinal cord barrier (BSCB), a neurovascular unit that limits passage of most agents from systemic circulation to the central nervous system, breaks down, resulting in inflammation, scar formation, and other sequelae. Protracted BSCB disruption may exacerbate cellular injury and hinder neurobehavioral recovery in SCI.

In these studies, angiopoietin-1 (Ang1), an agent known to reduce …