Robust Magnetic Resonance Imaging of Short T2 Tissues

Tissues with short transverse relaxation times are defined as ‘short T2 tissues’, and short T2 tissues often appear dark on images generated by conventional magnetic resonance imaging techniques. Common short T2 tissues include tendons, meniscus, and cortical bone. Ultrashort Echo Time (UTE) pulse sequences can provide morphologic contrasts and quantitative maps for short T2 tissues by reducing time-of-echo to the system minimum (e.g., less than 100 us). Therefore, UTE sequences have become a powerful imaging tool for visualizing and quantifying short T2 tissues in many applications. In this work, we developed a new Flexible Ultra Short time Echo (FUSE) pulse sequence employing a total of thirteen acquisition features with adjustable parameters, including optimized radiofrequency pulses, trajectories, choice of two or three dimensions, and multiple long-T2 suppression techniques. Together with the FUSE sequence, an improved analytical density correction and an auto-deblurring algorithm were incorporated as part of a novel reconstruction pipeline for reducing imaging artifacts. Firstly, we evaluated the FUSE sequence using a phantom containing short T2 components. The results demonstrated that differing UTE acquisition methods, improving the density correction functions and improving the deblurring algorithm could reduce the various artifacts, improve the overall signal, and enhance short T2 contrast. Secondly, we applied the FUSE sequence in bovine stifle joints (similar to the human knee) for morphologic imaging and quantitative assessment. The results showed that it was feasible to use the FUSE sequence to create morphologic images that isolate signals from the various knee joint tissues and carry out comprehensive quantitative assessments, using the meniscus as a model, including the mappings of longitudinal relaxation (T1) times, quantitative magnetization transfer parameters, and effective transverse relaxation (T2*) times. Lastly, we utilized the FUSE sequence to image the human skull for evaluating its feasibility in synthetic computed tomography (CT) generation and radiation treatment planning. The results demonstrated that the radiation treatment plans created using the FUSE-based synthetic CT and traditional CT data were able to present comparable dose calculations with the dose difference of mean less than a percent. In summary, this thesis clearly demonstrated the need for the FUSE sequence and its potential for robustly imaging short T2 tissues in various applications

Magnetic Resonance Imaging of Short-T2 Tissues with Applications for Quantifying Cortical Bone Water and Myelin

The human body contains a variety of tissue species with short T2 ranging from a few microseconds to hundreds of microseconds. Detection and quantification of these short-T2 species is of considerable clinical and scientific interest. Cortical bone water and myelin are two of the most important tissue constituents. Quantification of cortical bone water concentration allows for indirect estimation of bone pore volume and noninvasive assessment of bone quality. Myelin is essential for the proper functioning of the central nervous system (CNS). Direct assessment of myelin would reveal CNS abnormalities and enhance our understanding of neurological diseases. However, conventional MRI with echo times of several milliseconds or longer is unable to detect these short-lived MR signals. Recent advances in MRI technology and hardware have enabled development of a number of short-T2 imaging techniques, key among which are ultra-short echo time (UTE) imaging, zero echo time (ZTE) imaging, and sweep imaging with Fourier transform (SWIFT). While these pulse sequences are able to detect short-T2 species, they still suffer from signal interference between different T2 tissue constituents, image artifacts and excessive scan time. These are primary technical hurdles for application to whole-body clinical scanners. In this thesis research, new MRI techniques for improving short-T2 tissue imaging have been developed to address these challenges with a focus on direct detection and quantification of cortical bone water and myelin on a clinical MRI scanner. The first focus of this research was to optimize long-T2 suppression in UTE imaging. Saturation and adiabatic RF pulses were designed to achieve maximum long-T2 suppression while maximizing the signal from short-T2 species. The imaging protocols were optimized by Bloch equation simulations and were validated using phantom and in vivo experiments. The results show excellent short-T2 contrast with these optimized pulse sequences. The problem of blurring artifacts resulting from the inhomogeneous excitation profile of the rectangular pulses in ZTE imaging was addressed. The proposed approach involves quadratic phase-modulated RF excitation and iterative solution of an inverse problem formulated from the signal model of ZTE imaging and is shown to effectively remove the image artifacts. Subsequently image acquisition efficiency was improved in order to attain clinically-feasible scan times. To accelerate the acquisition speed in UTE and ZTE imaging, compressed sensing was applied with a hybrid 3D UTE sequence. Further, the pulse sequence and reconstruction procedure were modified to enable anisotropic field-of-view shape conforming to the geometry of the elongated imaged object. These enhanced acquisition techniques were applied to the detection and quantification of cortical bone water. A new biomarker, the suppression ratio (a ratio image derived from two UTE images, one without and the other with long-T2 suppression), was conceived as a surrogate measure of cortical bone porosity. Experimental data suggest the suppression ratio may be a more direct measure of porosity than previously measured total bone water concentration. Lastly, the feasibility of directly detecting and quantifying spatially-resolved myelin concentration with a clinical imager was explored, both theoretically and experimentally. Bloch equation simulations were conducted to investigate the intrinsic image resolution and the fraction of detectable myelin signal under current scanner hardware constraints. The feasibility of quantitative ZTE imaging of myelin extract and lamb spinal cord at 3T was demonstrated. The technological advances achieved in this dissertation research may facilitate translation of short-T2 MRI methods from the laboratory to the clinic

Novel MRI Technologies for Structural and Functional Imaging of Tissues with Ultra-short T₂ Values

Conventional MRI has several limitations such as long scan durations, motion artifacts, very loud acoustic noise, signal loss due to short relaxation times, and RF induced heating of electrically conducting objects. The goals of this work are to evaluate and improve the state-of-the-art methods for MRI of tissue with short T₂, to prove the feasibility of in vivo Concurrent Excitation and Acquisition, and to introduce simultaneous electroglottography measurement during functional lung MRI

A method of decoupling of radio frequency coils in magnetic resonance imaging : application to MRI with ultra short echo time concurrent excitation and acquisition

Ankara : The Department of Electrical and Electronics Engineering and the Graduate School of Engineering and Science of Bilkent University, 2013.Thesis (Master's) -- Bilkent University, 2013.Includes bibliographical references leaves 50-55.In this thesis, it was both experimentally and theoretically shown that decoupling of transmit and receive coils can be achieved by using a transmit array system such that individual currents induced from transmit coils will cancel each other resulting in a significantly reduced coupling. A novel method for decoupling of radio frequency (RF) coils was developed and implemented in a transmit array system with multiple transmit coil elements driven by RF current sources of different amplitude and phase. It was shown that this method for decoupling provides isolation over 70dB between transmit and receive coils. Decoupling procedure was described and its performance was analyzed in terms of obtained isolation. It was shown that MR signal can be detected during RF excitation with the achieved amount of decoupling. NMR spectroscopy and MRI with concurrent excitation and acquisition (CEA) was implemented. As an alternative to existing CEA methods, this method reduces dynamic range requirements so that CEA sequences can be applied in standard MRI scanners with minimal hardware modification. It was also demonstrated that this method can be used to implement ultra-short echo time (UTE) imaging with shorter acquisition delay. For CEA approach, acquired raw data was formulated as convolution of the free induction decay (FID) signal and the input B1 field. First proof of concept images were reconstructed from nonuniformly sampled k space data using both UTE and CEA sequences. UTE and CEA were shown to be feasible to implement using the same custom made decoupling setup in a clinical 3T MRI scanner. Significance of imaging of samples with ultra short T2* values was discussed.Özen, Ali ÇağlarM.S

Novel MRI Technologies for Structural and Functional Imaging of Tissues with Ultra-short T2 Values

Conventional MRI has several limitations such as long scan durations, motion artifacts, very high acoustic noise levels, signal loss due to short relaxation times, and RF induced heating of electrically conducting objects. The goals of this thesis are to evaluate state-of-the-art methods for MRI of tissue with short relaxation times, to prove the feasibility of CEA in a clinical MRI system, and to introduce a new electrophysiological measurement unit applied simultaneously with lung MRI

Absolute Quantitation for MR Molecular Imaging of Angiogenesis

Medical imaging is undergoing a transition from an art that is used to make static images of human physiology into a scientific tool that employs advanced techniques to measure clinically relevant data. Recently, the role of magnetic resonance imaging in cardiovascular and oncological research has grown, largely due to the implementation of new quantitative techniques in the clinic. Magnetic resonance imaging (MRI) and spectroscopy (MRS) are particularly rich in their capability to quantify both physiology and disease via biomarker detection. While this is true for many applications of MRI in cardiovascular and oncological research, 19F MR molecular imaging is particularly useful when coupled to the use of emerging site-targeted molecular imaging agents for diagnosis and therapy, such as αvβ3 integrin-targeted perfluorocarbon (PFC) nanoparticle (NP) emulsions. Unfortunately, the radiological world is realizing that although image quality may be consistently high, the absolute quantitative values being calculated vary widely across time, techniques, laboratories, and imaging platforms. The overall objective of this work is to advance the state of the art for 19F MR molecular imaging of perfluorocarbon nanoparticle emulsion contrast agents. To reach this objective, three specific aims have been identified: (1) to create new tools and techniques for 19F MR molecular imaging of PFC nanoparticles, (2) to develop translatable procedures for absolute quantification of 19F nuclei with MR molecular imaging, and (3) to evaluate the potential for clinical translation with ex vivo and in vivo preclinical experiments. Robust, standardized techniques are developed in this work to improve the accuracy of in vivo quantitative 19F MR molecular imaging, validate system performance, calibrate measurements to ensure repeatability of these quantitative metrics, and evaluate the potential for clinical translation. As these quantitative metrics become routine in medical imaging procedures, these standardized calibrations and techniques are expected to be critical for accurate interpretation of underlying pathophysiology. This will also impact the development of new therapies and diagnostic techniques/agents by reducing the variability of image-based measurements, thereby increasing the impact of the studies and reducing the overall time and cost to translate new technologies into the clinic

Improved motion-correction for MRI with markerless face-tracking

Motion artifacts are a well-known problem in MRI. They can extensively reduce image sharpness and resolution, as well as obscure pathologic conditions, which will make the images not suitable for clinical or research purposes. Over the years, multiple motion correction methods have been proposed to compensate for motion artifacts in different MRI applications. In this thesis, we investigate methods to maximize the image quality of brain MR images at different motion regimes, with the goal of obtaining high-quality images in the case of large and continuous motion profiles as might be expected in some children or patients with movement disorders. We describe a new autofocusing algorithm to correct for in-plane translations and rotations without any previous information coming from motion tracking sources. Preliminary results show good motion compensation for 2D translations. However, we show how rotations cannot be accurately estimated at the present stage, which should be investigated in future studies. We analyse the extent of the motion parameters estimation accuracy of a navigator-based motion correction method using simulated data. The navigator relies on GRAPPA reconstruction of the highly accelerated navigator fat-volumes to estimate the motion parameters. Our results suggest that the fat-navigator is capable of compensating for large range of motion, as well as for fast and slow changes in the head position. Better correction is expected if GRAPPA weights are updated throughout the entire duration of the scan. The fat-navigator is then compared with another tracking technique based on structured light to track the subject’s head movements. We present the results obtained from different motion types as well as a method to improve the motion estimation accuracy of the navigator-based technique in the presence of extensive pitch-wise motion using a skull masking approach. Finally, we introduce a method to quickly develop and test motion-robust pulse sequences using an open-source framework to acquire MR images producing low acoustic noise levels, which make them suitable for paediatric/infant age group, where research scans are typically conducted while the subject is sleeping