Parallel MR Image Reconstruction Using Augmented Lagrangian Methods

Magnetic resonance image (MRI) reconstruction using SENSitivity Encoding (SENSE) requires regularization to suppress noise and aliasing effects. Edge-preserving and sparsity-based regularization criteria can improve image quality, but they demand computation-intensive nonlinear optimization. In this paper, we present novel methods for regularized MRI reconstruction from undersampled sensitivity encoded data-SENSE-reconstruction-using the augmented Lagrangian (AL) framework for solving large-scale constrained optimization problems. We first formulate regularized SENSE-reconstruction as an unconstrained optimization task and then convert it to a set of (equivalent) constrained problems using variable splitting. We then attack these constrained versions in an AL framework using an alternating minimization method, leading to algorithms that can be implemented easily. The proposed methods are applicable to a general class of regularizers that includes popular edge-preserving (e.g., total-variation) and sparsity-promoting (e.g., -norm of wavelet coefficients) criteria and combinations thereof. Numerical experiments with synthetic and in vivo human data illustrate that the proposed AL algorithms converge faster than both general-purpose optimization algorithms such as nonlinear conjugate gradient (NCG) and state-of-the-art MFISTA.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/85846/1/Fessler4.pd

Development of Advanced Acquisition and Reconstruction Techniques for Real-Time Perfusion MRI

Diese Doktorarbeit befasst sich mit der methodischen Entwicklung von Akquisition- und Rekonstruktionstechniken zur Anwendung von Echtzeit-Bildgebungstechniken auf das Gebiet der dynamischen kontrastmittelgestützten Magentresonanztomographie. Zur Unterdrückung unerwünschter Bildartefakte wird eine neue Spoiling-Technik vorgeschlagen, die auf randomisierten Phasen der Hochfrequenzanregung basiert. Diese Technik erlaubt eine schnelle, artefaktfreie Aufnahme von T1-gewichteten Rohdaten bei radialer Abtastung. Die Rekonstruktion quantitativer Parameterkarten aus solchen Rohdaten kann als nichtlineares, inverses Problem aufgefasst werden. In dieser Arbeit wird eine modellbasierte Rekonstruktionstechnik zur quantitativen T1-Kartierung entwickelt, die dieses inverse Problem mittels der iterativ regularisierten Gauß-Newton-Methode mit parameterspezifischer Regularisierung löst. In Simulationen sowie in-vitro- und in-vivo-Studien wird Genauigkeit und Präzision dieser neuen Methode geprüft, die ihre direkte Anwendung in in-vitro-Experimenten zur "first-pass"-Perfusion findet. In diesen Experimenten wird ein kommerziell verfügbares Phantom verwendet, dass in-vivo-Perfusion simuliert und gleichzeitig vollständige Kontrolle über die vorherrschenden Austauschraten erlaubt

MR image reconstruction using deep density priors

Algorithms for Magnetic Resonance (MR) image reconstruction from undersampled measurements exploit prior information to compensate for missing k-space data. Deep learning (DL) provides a powerful framework for extracting such information from existing image datasets, through learning, and then using it for reconstruction. Leveraging this, recent methods employed DL to learn mappings from undersampled to fully sampled images using paired datasets, including undersampled and corresponding fully sampled images, integrating prior knowledge implicitly. In this article, we propose an alternative approach that learns the probability distribution of fully sampled MR images using unsupervised DL, specifically Variational Autoencoders (VAE), and use this as an explicit prior term in reconstruction, completely decoupling the encoding operation from the prior. The resulting reconstruction algorithm enjoys a powerful image prior to compensate for missing k-space data without requiring paired datasets for training nor being prone to associated sensitivities, such as deviations in undersampling patterns used in training and test time or coil settings. We evaluated the proposed method with T1 weighted images from a publicly available dataset, multi-coil complex images acquired from healthy volunteers (N=8) and images with white matter lesions. The proposed algorithm, using the VAE prior, produced visually high quality reconstructions and achieved low RMSE values, outperforming most of the alternative methods on the same dataset. On multi-coil complex data, the algorithm yielded accurate magnitude and phase reconstruction results. In the experiments on images with white matter lesions, the method faithfully reconstructed the lesions. Keywords: Reconstruction, MRI, prior probability, machine learning, deep learning, unsupervised learning, density estimationComment: Published in IEEE TMI. Main text and supplementary material, 19 pages tota

Rosette Spectroscopic Imaging

Chemical shift imaging (CSI) has been the mainstay of spectroscopic imaging because of its simple implementation, reliability and ease of image reconstruction. This technique has been widely used for observing the changes in the metabolic signature of tissues during evolving pathological and/or physiological conditions. CSI owes its ease of implementation and analysis to the Fourier encoding approach upon which is based. In this approach, the spectral-spatial information is encoded in a rectilinear fashion that favors the acquisition of very high-resolution information along the spectral axis and relatively low resolution along the spatial directions. For applications where higher spatial resolution is desired over a narrower spectral bandwidth, trajectory designs that repeatedly cross the center of k-space through the use of time-dependent gradients offer a convenient means to achieve significant speedups in data acquisition. This stems from the fact that the readout period could be used to acquire multiple spatial frequency values which, in turn, leads to a reduction in the total number of RF excitations required to provide proper encoding of the spatial and spectral information. Among the trajectory designs that could be well suited for such a spectroscopic imaging approach the Rosette data acquisition approach is particularly attractive because of its relatively simple implementation and modest gradient requirements. The time-varying nature of the gradients in this trajectory design, while flexible, leads to smooth variations in sample density and larger signal bandwidths than those associated with the CSI gold standard. Despite these potential drawbacks, because no time is spent collecting information in the corners of k-space, we demonstrate that rosette spectroscopic imaging (RSI) can lead to an efficiency gain over CSI in a wide range of spectral bandwidths and spatial resolutions. An analytic relationship for the number of excitations to be used in an RSI experiment is derived and a method to obtain a more accurate self-derived B0 map that uses the information of the prevalent resonance in each voxel and linear regression is offered. Moreover, we show that any imaging technique that periodically samples the center and edges of k-space could be used for spectroscopic imaging

Rapid 3D Phase Contrast Magnetic Resonance Angiography through High-Moment Velocity Encoding and 3D Parallel Imaging

abstract: Phase contrast magnetic resonance angiography (PCMRA) is a non-invasive imaging modality that is capable of producing quantitative vascular flow velocity information. The encoding of velocity information can significantly increase the imaging acquisition and reconstruction durations associated with this technique. The purpose of this work is to provide mechanisms for reducing the scan time of a 3D phase contrast exam, so that hemodynamic velocity data may be acquired robustly and with a high sensitivity. The methods developed in this work focus on the reduction of scan duration and reconstruction computation of a neurovascular PCMRA exam. The reductions in scan duration are made through a combination of advances in imaging and velocity encoding methods. The imaging improvements are explored using rapid 3D imaging techniques such as spiral projection imaging (SPI), Fermat looped orthogonally encoded trajectories (FLORET), stack of spirals and stack of cones trajectories. Scan durations are also shortened through the use and development of a novel parallel imaging technique called Pretty Easy Parallel Imaging (PEPI). Improvements in the computational efficiency of PEPI and in general MRI reconstruction are made in the area of sample density estimation and correction of 3D trajectories. A new method of velocity encoding is demonstrated to provide more efficient signal to noise ratio (SNR) gains than current state of the art methods. The proposed velocity encoding achieves improved SNR through the use of high gradient moments and by resolving phase aliasing through the use measurement geometry and non-linear constraints.Dissertation/ThesisPh.D. Bioengineering 201

Simultaneous Multislice Functional Magnetic Resonance Imaging.

Functional magnetic resonance imaging (fMRI) is a valuable tool for mapping brain activity in many fields. Since functional activity is determined by temporal signal changes, undesired fluctuations from physiological motion are problematic. Simultaneous multislice (SMS) imaging can alleviate these issues by accelerating image acquisition, increasing the temporal resolution. Furthermore, some applications require a temporal resolution higher than what conventional fMRI will allow. Current research in SMS has focused on Cartesian readouts due to their ease in analysis and reconstruction. However, non-Cartesian readouts such as spirals have shorter readout times and better signal recovery. This work explores the acquisition and reconstruction of both spiral and concentric ring readouts in parallel SMS. The concentric ring readout retains most of the benefits of spirals, but also increases the usability of alternative reconstruction techniques for non-Cartesian SMS such as generalized autocalibrating partially parallel acquisitions (GRAPPA). To date, non-Cartesian SMS imaging has only been reconstructed with sensitivity encoding (SENSE), but results in this work indicate GRAPPA-based reconstructions have reduced root-mean-square-error compared to SENSE and good subjective image quality as well. Furthermore, using point spread function analysis, the concentric ring trajectory is found to have superior slice separation properties compared to a spiral one. Since parallel imaging greatly magnifies the amount of data used for reconstruction, a novel coil compression method is developed, which outperforms conventional coil compression in fMRI, substantially decreasing the amount of reconstruction time needed for sufficient detection of functional activation. Results indicate that the proposed method can compress 3 simultaneous slice data using a 32-channel coil down to only 10 virtual coils without any adverse effects in functional activation, noise, or image artifacts. Competing methods require substantially more coils for preservation of the data, resulting in large reconstruction time savings for the proposed method. This work also explores the use of Hadamard-encoded fMRI for increased temporal resolution. Because Hadamard-encoded SMS uses data from multiple time frames to separate slices, physiological noise correction is critical. However, even with physiological noise correction, results indicate Hadamard-encoded fMRI is not as reliable as conventional fMRI due to undesired temporal fluctuations, most notably from uncorrected physiological noise.PhDBiomedical EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/120669/1/alanchu_1.pd

Doctor of Philosophy

dissertationCine phase contrast (PC) magnetic resonance imaging (MRI) is a useful imaging technique that allows for the quantitative measurement of in-vivo blood velocities over the cardiac cycle. Velocity information can be used to diagnose and learn more about the mechanisms of cardio-vascular disease. Compared to other velocity measuring techniques, PC MRI provides high-resolution 2D and 3D spatial velocity information. Unfortunately, as with many other MRI techniques, PC MRI su ers from long acquisition times which places constraints on temporal and spatial resolution. This dissertation outlines the use of temporally constrained reconstruction (TCR) of radial PC data in order to signi cantly reduce the acquisition time so that higher temporal and spatial resolutions can be achieved. A golden angle-based acquisition scheme and a novel self-gating method were used in order to allow for exible selection of temporal resolution and to ameliorate the di culties associated with external electrocardiogram (ECG) gating. Finally, image reconstruction times for TCR are signi cantly reduced by implementation on a high-performance computer cluster. The TCR algorithm is executed in parallel across multiple GPUs achieving a 50 second reconstruction time for a very large cardiac perfusion data set