Accelerated Imaging Techniques for Chemical Shift Magnetic Resonance Imaging

Chemical shift imaging is a method for the separation two or more chemical species. The cost of chemical shift encoding is increased acquisition time as multiple acquisitions are acquired at different echo times. Image acceleration techniques, typically parallel imaging, are often used to improve the spatial coverage and resolution. This thesis describes a new technique for estimating the signal to noise ratio for parallel imaging reconstructions and proposes new image reconstructions for accelerated chemical shift imaging using compressed sensing and/or parallel imaging for two applications: water-fat separation and metabolic imaging of hyperpolarized [1-13C] pyruvate. Spatially varying noise in parallel imaging reconstructions makes measurements of the signal to noise ratio, a commonly used metric for image for image quality, difficult. Existing approaches have limitations such as they are not applicable to all reconstructions, require significant computation time, or rely on repeated image acquisitions. A SNR estimation technique is proposed that does not exhibit these limitations. Water-fat imaging of highly undersampled datasets from the liver, calf, knee, and abdominal cavity are demonstrated using a customized IDEAL-SPGR pulse sequence and an integrated compressed sensing, parallel imaging, water-fat reconstruction. This method is shown to offer comparable image quality relative to fully sampled reference images for a range of acceleration factors. At high acceleration factors, this technique is shown to offer improved image quality when compared to the current standard of parallel imaging. Accelerated chemical shift imaging was demonstrated for metabolic of hyperpolarized [1-13C] pyruvate. Pyruvate, lactate, alanine, and bicarbonate images were reconstructed from undersampled datasets. Phantoms were used to validate this technique while retrospectively and prospectively accelerated 3D in vivo datasets were used to demonstrate. Alternatively, acceleration was also achieved through the use of a high performance magnetic field gradient set. This thesis addresses the inherently slow acquisition times of chemical shift imaging by examining the role compressed sensing and parallel imaging can be play in chemical shift imaging. An approach to SNR assessment for parallel imaging reconstruction is proposed and approaches to accelerated chemical shift imaging are described for applications in water-fat imaging and metabolic imaging of hyperpolarized [1-13C] pyruvate

Compressed Sensing Accelerated Magnetic Resonance Spectroscopic Imaging

abstract: Magnetic resonance spectroscopic imaging (MRSI) is a valuable technique for assessing the in vivo spatial profiles of metabolites like N-acetylaspartate (NAA), creatine, choline, and lactate. Changes in metabolite concentrations can help identify tissue heterogeneity, providing prognostic and diagnostic information to the clinician. The increased uptake of glucose by solid tumors as compared to normal tissues and its conversion to lactate can be exploited for tumor diagnostics, anti-cancer therapy, and in the detection of metastasis. Lactate levels in cancer cells are suggestive of altered metabolism, tumor recurrence, and poor outcome. A dedicated technique like MRSI could contribute to an improved assessment of metabolic abnormalities in the clinical setting, and introduce the possibility of employing non-invasive lactate imaging as a powerful prognostic marker. However, the long acquisition time in MRSI is a deterrent to its inclusion in clinical protocols due to associated costs, patient discomfort (especially in pediatric patients under anesthesia), and higher susceptibility to motion artifacts. Acceleration strategies like compressed sensing (CS) permit faithful reconstructions even when the k-space is undersampled well below the Nyquist limit. CS is apt for MRSI as spectroscopic data are inherently sparse in multiple dimensions of space and frequency in an appropriate transform domain, for e.g. the wavelet domain. The objective of this research was three-fold: firstly on the preclinical front, to prospectively speed-up spectrally-edited MRSI using CS for rapid mapping of lactate and capture associated changes in response to therapy. Secondly, to retrospectively evaluate CS-MRSI in pediatric patients scanned for various brain-related concerns. Thirdly, to implement prospective CS-MRSI acquisitions on a clinical magnetic resonance imaging (MRI) scanner for fast spectroscopic imaging studies. Both phantom and in vivo results demonstrated a reduction in the scan time by up to 80%, with the accelerated CS-MRSI reconstructions maintaining high spectral fidelity and statistically insignificant errors as compared to the fully sampled reference dataset. Optimization of CS parameters involved identifying an optimal sampling mask for CS-MRSI at each acceleration factor. It is envisioned that time-efficient MRSI realized with optimized CS acceleration would facilitate the clinical acceptance of routine MRSI exams for a quantitative mapping of important biomarkers.Dissertation/ThesisDoctoral Dissertation Bioengineering 201

Advanced H-1 Lung Magnetic Resonance Imaging

Magnetic resonance imaging (MRI) is one of the widely used medical imaging modality, since it can provide both structural and functional assessment in a single imaging session. However, two major challenges should be considered by using MRI for lung imaging. The first challenge is the intrinsic low SNR of H-1 lung MRI due to the low proton density as well as the fast decay of the lung parenchyma signal. And the second challenge is subject motion. To achieve high resolution structural image, MRI requires a long scan time, usually a few minutes or even longer, which make MRI sensitive to subject motion. To address the first challenge, ultra-short echo time (UTE) MRI sequence is used to capture the lung parenchyma signal before decay. As for subject motion, two major strategies are widely used. One strategy is fast breath-holding scan, the subjects are asked to hold their breaths for a short duration, and the fast 3D MR sequence would be used to acquire data within that duration. This dissertation proposes a new acquisition scheme based on the standard UTE sequence, which largely increases the encoding efficiency and improves the breath-holding scan images. The other is free breathing scan with motion correction. The subjects are allowed to breathe during the MR acquisition. After the acquisition, the motion corrupted data would go through the motion correction step to reconstruct the motion free images. In this dissertation, two novel motion corrected reconstruction strategies are proposed to incorporate the motion modeling and compensation into the reconstruction to get high SNR motion corrected 3D and 4D images. When translating the developed techniques to the clinical studies, specifically for pediatric and neonatal studies, more practical problems need to be considered, such as smaller but finer anatomy to image, the different respiratory patterns of the young subjects etc. This dissertation proposes a 5-minute free breathing UTE MRI strategy to achieve a 3D high resolution motion free lung image for pediatric and neonatal studies

Entwicklung und Anwendung der in vivo abdominellen Magnetresonanzelastographie

Magnetic Resonance Elastography (MRE) is a well-established non-invasive imaging technique used to quantify the mechanical properties of tissues in vivo for the diagnosis of liver fibrosis. However, MRE is limited by its spatial resolution, sensitivity to motion artifacts, and insensitivity to metabolic function. Therefore, three studies of abdominal MRE were conducted to improve the quality of mechanical maps for characterizing liver tumors, to correct for motion artifacts induced by breathing, and to implement MRE on a PET/MRI scanner to correlate mechanical liver properties with metabolic functions in small animals through technical improvements in image acquisition and post-processing. High-resolution stiffness (shear wave speed in m/s), wave penetration (penetration rate in m/s), and fluidity (phase of the complex shear modulus in rad) maps were generated using multifrequency MRE, novel actuators, and tomoelastography post-processing. The first study characterized the stiffness and fluidity of a total of 141 liver tumors in 70 patients. The second study analyzed the motion of abdominal organs and its effect on their stiffness using different acquisition paradigms and image registration in 12 subjects. The third study examined the relationship of liver stiffness and wave penetration to central metabolic liver functions in 19 rabbits. Malignant liver tumors were distinguished from the surrounding liver (stiffness area under the curve [AUC]: 0.88 and fluidity AUC: 0.95) and benign tumors (stiffness AUC: 0.85 and fluidity AUC: 0.86) due to their increased stiffness and fluidity. In the second study, no significant differences in stiffness were observed despite significant differences in examination time, organ motion, and image quality with different image acquisition paradigms. Motion correction by image registration increased image sharpness, so that no significant difference was measurable between MRE in free breathing and breath-hold. Healthy rabbit livers showed heterogeneous liver stiffness, such that division into low and high stiffness (>1.6 m/s) groups resulted in significant differences in central metabolic functions. Stiffness and fluidity measured by multifrequency MRE hold promise as quantitative biomarkers for the diagnosis of malignant liver tumors. Abdominal MRE with free breathing, followed by image registration, is recommended as the best balance between fast examination time and good image quality. Additionally, the applicability of abdominal MRE in small animals in a clinical MRI was demonstrated, and correlations between mechanical liver properties and metabolic functions were found. This study demonstrates improvements in the quality of maps of biophysical parameters for both clinical and preclinical studies, making an important contribution to the clinical translation of multifrequency MRE as a non-invasive imaging modality for abdominal organs and pathologies.Die Magnetresonanzelastographie (MRE) ist eine nichtinvasive Bildgebungsmethode zur Quantifizierung mechanischer Gewebeeigenschaften in vivo bei der Diagnose von Leberfibrose. Limitationen bestehen aufgrund örtlicher Bildauflösung, Bewegungsempfindlichkeit und Insensitivität zu metabolischen Funktionen. Aufgrund technischer Verbesserung in der Bildaufnahme und der Bildauswertung wurde daher anhand von drei Studien zur abdominellen MRE die Bildqualität mechanischer Karten zur Charakterisierung von Lebertumoren verbessert, atmungsinduzierte Organbewegungen korrigiert und die MRE an klinischen PET/MRT implementiert, um an Kleintieren die mechanischen Lebereigenschaften mit metabolischen Funktionen zu korrelieren. Mittels multifrequenter MRE, neuartiger Aktoren und tomoelastographischer Auswertung wurden hochaufgelöste Karten der Steifigkeit (Scherwellengeschwindigkeit in m/s), Wellenpenetration (Wellenpenetrationsrate in m/s) und Fluidität (Phase des komplexen Schermoduls in rad) generiert. Die erste Studie charakterisierte die Steifigkeit und Fluidität von insgesamt 141 Lebertumoren an 70 Patienten. Eine zweite Studie analysierte die Bewegung und den Einfluss auf die Steifigkeit abdomineller Organe mittels unterschiedlicher Aufnahmeparadigmen und Bildregistrierung in 12 Probanden. In einer dritten Studie wurde der Zusammenhang von Lebersteifigkeit und Wellenpenetration zu zentralen metabolischen Leberfunktionen an 19 Kaninchen untersucht. Maligne Lebertumoren können durch erhöhte Steifigkeit und Fluidität (Steifigkeit AUC: 0.88 und Fluidität AUC: 0.95) gut von gutartigen Tumoren (Steifigkeit AUC: 0.85 und Fluidität AUC: 0.86) unterschieden werden. In der zweiten Studie wurden trotz verschiedener Aufnahmeparadigmen und Unterschiede in Untersuchungsdauer, Organbewegung und Bildqualität keine signifikanten Unterschiede in der Organsteifigkeit festgestellt. Die Bildregistrierung verbesserte die Bildschärfe, sodass kein signifikanter Unterschied zwischen freier Atmung und Atempause messbar war. Kaninchenlebern zeigten heterogene Steifigkeiten, sodass eine Zweiteilung in niedrige und hohe Steifigkeit (>1.6 m/s) signifikante Unterschiede in zentralen metabolischen Funktionen zeigte. Steifigkeit und Fluidität, die mittels der Mehrfrequenz-MRE gemessen werden, stellen vielversprechende quantitative Biomarker für die Diagnose maligner Lebertumoren dar. Abdominelle MRE in freier Atmung mit Bildregistrierung ist der beste Kompromiss aus schneller Untersuchungsdauer und guter Bildqualität. Die Anwendbarkeit an Kleintieren in einem klinischen MRT wurde gezeigt, inklusive Korrelationen zwischen mechanischen Lebereigenschaften und metabolischen Funktionen. Diese Arbeit konnte somit die Bildqualität mechanischer Karten sowohl für klinische als auch präklinische Untersuchungen verbessern und damit einen wichtigen Beitrag zur Translation der Multifrequenz-MRE als klinisch angewandte nichtinvasive Bildgebungsmethode abdomineller Organe und Pathologien leisten

Acceleration of Subtractive Non-contrast-enhanced Magnetic Resonance Angiography

Although contrast-enhanced magnetic resonance angiography (CE-MRA) is widely established as a clinical examination for the diagnosis of human vascular diseases, non-contrast-enhanced MRA (NCE-MRA) techniques have drawn increasing attention in recent years. NCE-MRA is based on the intrinsic physical properties of blood and does not require the injection of any exogenous contrast agents. Subtractive NCE-MRA is a class of techniques that acquires two image sets with different vascular signal intensity, which are later subtracted to generate angiograms. The long acquisition time is an important drawback of NCE-MRA techniques, which not only limits the clinical acceptance of these techniques but also renders them sensitive to artefacts from patient motion. Another problem for subtractive NCE-MRA is the unwanted residual background signal caused by different static background signal levels on the two raw image sets. This thesis aims at improving subtractive NCE-MRA techniques by addressing both these limitations, with a particular focus on three-dimensional (3D) femoral artery fresh blood imaging (FBI). The structure of the thesis is as follows: Chapter 1 describes the anatomy and physiology of the vascular system, including the characteristics of arteries and veins, and the MR properties and flow characteristics of blood. These characteristics are the foundation of NCE-MRA technique development. Chapter 2 introduces commonly used diagnostic angiographic methods, particularly CE-MRA and NCE-MRA. Current NCE-MRA techniques are reviewed and categorised into different types. Their principles, implementations and limitations are summarised. Chapter 3 describes imaging acceleration theories including compressed sensing (CS), parallel imaging (PI) and partial Fourier (PF). The Split Bregman algorithm is described as an efficient CS reconstruction method. The SPIRiT reconstruction for PI and homodyne detection for PF are also introduced and combined with Split Bregman to form the basis of the reconstruction strategy for undersampled MR datasets. Four image quality metrics are presented for evaluating the quality of reconstructed images. In Chapter 4, an intensity correction method is proposed to improve background suppression for subtractive NCE-MRA techniques. Residual signals of background tissues are removed by performing a weighted subtraction, in which the weighting factor is obtained by a robust regression method. Image sparsity can also be increased and thereby potentially benefit CS reconstruction in the following chapters. Chapter 5 investigates the optimal k-space sampling patterns for the 3D accelerated femoral artery FBI sequence. A variable density Poisson-disk with a fully sampled centre region and missing partial Fourier fractions is employed for k-space undersampling in the ky-kz plane. Several key parameters in sampling pattern design, such as partial Fourier sampling ratios, fully sampled centre region size and density decay factor, are evaluated and optimised. Chapter 6 introduces several reconstruction strategies for accelerated subtractive NCE-MRA. A new reconstruction method, k-space subtraction with phase and intensity correction (KSPIC), is developed. By performing subtraction in k-space, KSPIC can exploit the sparsity of subtracted angiogram data and potentially improve the reconstruction performance. A phase correction procedure is used to restore the polarity of negative signals caused by subtraction. The intensity correction method proposed in Chapter 4 is also incorporated in KSPIC as it improves background suppression and thereby sparsity. The highly accelerated technique can be used not only to reduce the acquisition time, but also to enable imaging with increased resolution with no time penalty. A time-efficient high-resolution FBI technique is proposed in Chapter 7. By employing KSPIC and modifying the flow-compensation/spoiled gradients, the image matrix size can be increased from 256×256 to up to 512×512 without prolonging the acquisition time. Chapter 8 summarises the overall achievements and limitations of this thesis, as well as outlines potential future research directions.Cambridge Trust China Scholarship Council Addenbrooke’s Charitable Trust National Institute of Health Research, Cambridge Biomedical Research Cente

Advanced Image Acquisition, Processing Techniques and Applications

"Advanced Image Acquisition, Processing Techniques and Applications" is the first book of a series that provides image processing principles and practical software implementation on a broad range of applications. The book integrates material from leading researchers on Applied Digital Image Acquisition and Processing. An important feature of the book is its emphasis on software tools and scientific computing in order to enhance results and arrive at problem solution

Mri Methods For Imaging The Feto-Placental Vasculature And Blood

Fetal magnetic resonance imaging (MRI) in recent times has become a well-established adjunct to ultrasound (US) in routine clinical prenatal care and diagnostics. The majority of fetal MRI is restricted to T2-weighted scans, where the diagnosis is based on the appearance of normal and abnormal tissue. Although there have been many advancements in MRI and a plethora of sequences, that probe different anatomical and different physiological process, the adaptation of these in fetal imaging has been rather slow. Many of these can extract quantitative parameters that can throw light on the underlying tissue’s normal/patho-physiology. But the use of such quantitative MRI methods has been extremely limited in fetal imaging due to its unique and dynamic physiological milieu that pose several technical challenges including low signal to noise and/or resolution, artifacts associated with abdominal imaging and most importantly fetal motion. These limitations are expected to be overcome by (a) optimizing and (b) developing novel MR imaging sequences, both of which constitute the primary aim of my work. This work develops a framework that allows for vascular imaging in the fetus and placenta. This includes both qualitative vascular imaging and blood flow quantification. Towards this, three broad directions were explored (a) Moving to higher field imaging, while optimizing parameters for low energy deposition and (b) application of non-gated phase contrast MRI and (c) optimization of conventional time-of-flight angiography for fetal applications

Doctor of Philosophy

dissertationDynamic contrast enhanced magnetic resonance imaging (DCE-MRI) is a powerful tool to detect cardiac diseases and tumors, and both spatial resolution and temporal resolution are important for disease detection. Sampling less in each time frame and applying sophisticated reconstruction methods to overcome image degradations is a common strategy in the literature. In this thesis, temporal TV constrained reconstruction that was successfully applied to DCE myocardial perfusion imaging by our group was extended to three-dimensional (3D) DCE breast and 3D myocardial perfusion imaging, and the extension includes different forms of constraint terms and various sampling patterns. We also explored some other popular reconstruction algorithms from a theoretical level and showed that they can be included in a unified framework. Current 3D Cartesian DCE breast tumor imaging is limited in spatiotemporal resolution as high temporal resolution is desired to track the contrast enhancement curves, and high spatial resolution is desired to discern tumor morphology. Here temporal TV constrained reconstruction was extended and different forms of temporal TV constraints were compared on 3D Cartesian DCE breast tumor data with simulated undersampling. Kinetic parameters analysis was used to validate the methods