Low-rank and sparse reconstruction in dynamic magnetic resonance imaging via proximal splitting methods

Dynamic magnetic resonance imaging (MRI) consists of collecting multiple MR images in time, resulting in a spatio-temporal signal. However, MRI intrinsically suffers from long acquisition times due to various constraints. This limits the full potential of dynamic MR imaging, such as obtaining high spatial and temporal resolutions which are crucial to observe dynamic phenomena. This dissertation addresses the problem of the reconstruction of dynamic MR images from a limited amount of samples arising from a nuclear magnetic resonance experiment. The term limited can be explained by the approach taken in this thesis to speed up scan time, which is based on violating the Nyquist criterion by skipping measurements that would be normally acquired in a standard MRI procedure. The resulting problem can be classified in the general framework of linear ill-posed inverse problems. This thesis shows how low-dimensional signal models, specifically lowrank and sparsity, can help in the reconstruction of dynamic images from partial measurements. The use of these models are justified by significant developments in signal recovery techniques from partial data that have emerged in recent years in signal processing. The major contributions of this thesis are the development and characterisation of fast and efficient computational tools using convex low-rank and sparse constraints via proximal gradient methods, the development and characterisation of a novel joint reconstruction–separation method via the low-rank plus sparse matrix decomposition technique, and the development and characterisation of low-rank based recovery methods in the context of dynamic parallel MRI. Finally, an additional contribution of this thesis is to formulate the various MR image reconstruction problems in the context of convex optimisation to develop algorithms based on proximal splitting methods

Dependent Nonparametric Bayesian Group Dictionary Learning for online reconstruction of Dynamic MR images

In this paper, we introduce a dictionary learning based approach applied to the problem of real-time reconstruction of MR image sequences that are highly undersampled in k-space. Unlike traditional dictionary learning, our method integrates both global and patch-wise (local) sparsity information and incorporates some priori information into the reconstruction process. Moreover, we use a Dependent Hierarchical Beta-process as the prior for the group-based dictionary learning, which adaptively infers the dictionary size and the sparsity of each patch; and also ensures that similar patches are manifested in terms of similar dictionary atoms. An efficient numerical algorithm based on the alternating direction method of multipliers (ADMM) is also presented. Through extensive experimental results we show that our proposed method achieves superior reconstruction quality, compared to the other state-of-the- art DL-based methods

Accelerated Cardiac Diffusion Tensor Imaging Using Joint Low-Rank and Sparsity Constraints

Objective: The purpose of this manuscript is to accelerate cardiac diffusion tensor imaging (CDTI) by integrating low-rankness and compressed sensing. Methods: Diffusion-weighted images exhibit both transform sparsity and low-rankness. These properties can jointly be exploited to accelerate CDTI, especially when a phase map is applied to correct for the phase inconsistency across diffusion directions, thereby enhancing low-rankness. The proposed method is evaluated both ex vivo and in vivo, and is compared to methods using either a low-rank or sparsity constraint alone. Results: Compared to using a low-rank or sparsity constraint alone, the proposed method preserves more accurate helix angle features, the transmural continuum across the myocardium wall, and mean diffusivity at higher acceleration, while yielding significantly lower bias and higher intraclass correlation coefficient. Conclusion: Low-rankness and compressed sensing together facilitate acceleration for both ex vivo and in vivo CDTI, improving reconstruction accuracy compared to employing either constraint alone. Significance: Compared to previous methods for accelerating CDTI, the proposed method has the potential to reach higher acceleration while preserving myofiber architecture features which may allow more spatial coverage, higher spatial resolution and shorter temporal footprint in the future.Comment: 11 pages, 16 figures, published on IEEE Transactions on Biomedical Engineerin

Magnetic resonance image reconstruction using trained geometric directions in 2D redundant wavelets domain and non-convex optimization

Reducing scanning time is significantly important for MRI. Compressed sensing has shown promising results by undersampling the k-space data to speed up imaging. Sparsity of an image plays an important role in compressed sensing MRI to reduce the image artifacts. Recently, the method of patch-based directional wavelets (PBDW) which trains geometric directions from undersampled data has been proposed. It has better performance in preserving image edges than conventional sparsifying transforms. However, obvious artifacts are presented in the smooth region when the data are highly undersampled. In addition, the original PBDW-based method does not hold obvious improvement for radial and fully 2D random sampling patterns. In this paper, the PBDW-based MRI reconstruction is improved from two aspects: 1) An efficient non-convex minimization algorithm is modified to enhance image quality; 2) PBDW are extended into shift-invariant discrete wavelet domain to enhance the ability of transform on sparsifying piecewise smooth image features. Numerical simulation results on vivo magnetic resonance images demonstrate that the proposed method outperforms the original PBDW in terms of removing artifacts and preserving edges

Robust Algorithms for Low-Rank and Sparse Matrix Models

Data in statistical signal processing problems is often inherently matrix-valued, and a natural first step in working with such data is to impose a model with structure that captures the distinctive features of the underlying data. Under the right model, one can design algorithms that can reliably tease weak signals out of highly corrupted data. In this thesis, we study two important classes of matrix structure: low-rankness and sparsity. In particular, we focus on robust principal component analysis (PCA) models that decompose data into the sum of low-rank and sparse (in an appropriate sense) components. Robust PCA models are popular because they are useful models for data in practice and because efficient algorithms exist for solving them. This thesis focuses on developing new robust PCA algorithms that advance the state-of-the-art in several key respects. First, we develop a theoretical understanding of the effect of outliers on PCA and the extent to which one can reliably reject outliers from corrupted data using thresholding schemes. We apply these insights and other recent results from low-rank matrix estimation to design robust PCA algorithms with improved low-rank models that are well-suited for processing highly corrupted data. On the sparse modeling front, we use sparse signal models like spatial continuity and dictionary learning to develop new methods with important adaptive representational capabilities. We also propose efficient algorithms for implementing our methods, including an extension of our dictionary learning algorithms to the online or sequential data setting. The underlying theme of our work is to combine ideas from low-rank and sparse modeling in novel ways to design robust algorithms that produce accurate reconstructions from highly undersampled or corrupted data. We consider a variety of application domains for our methods, including foreground-background separation, photometric stereo, and inverse problems such as video inpainting and dynamic magnetic resonance imaging.PHDElectrical Engineering: SystemsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/143925/1/brimoor_1.pd

Superresolution Reconstruction for Magnetic Resonance Spectroscopic Imaging Exploiting Low-Rank Spatio-Spectral Structure

Magnetic resonance spectroscopic imaging (MRSI) is a rapidly developing medical imaging modality, capable of conferring both spatial and spectral information content, and has become a powerful clinical tool. The ability to non-invasively observe spatial maps of metabolite concentrations, for instance, in the human brain, can offer functional, as well as pathological insights, perhaps even before structural aberrations or behavioral symptoms are evinced. Despite its lofty clinical prospects, MRSI has traditionally remained encumbered by a number of practical limitations. Of primary concern are the vastly reduced concentrations of tissue metabolites when compared to that of water, which forms the basis for conventional MR imaging. Moreover, the protracted exam durations required by MRSI routinely approach the limits for patient compliance. Taken in conjunction, the above considerations effectively circumscribe the data collection process, ultimately translating to coarse image resolutions that are of diminished clinical utility. Such shortcomings are compounded by spectral contamination artifacts due to the system pointspread function, which arise as a natural consequence when reconstructing non-band-limited data by the inverse Fourier transform. These artifacts are especially pronounced near regions characterized by substantial discrepancies in signal intensity, for example, the interface between normal brain and adipose tissue, whereby the metabolite signals are inundated by the dominant lipid resonances. In recent years, concerted efforts have been made to develop alternative, non-Fourier MRSI reconstruction strategies that aim to surmount the aforementioned limitations. In this dissertation, we build upon the burgeoning medley of innovative and promising techniques, proffering a novel superresolution reconstruction framework predicated on the recent interest in low-rank signal modeling, along with state-of-the-art regularization methods. The proposed framework is founded upon a number of key tenets. Firstly, we proclaim that the underlying spatio-spectral distribution of the investigated object admits a bilinear representation, whereby spatial and spectral signal components can be effectively segregated. We further maintain that the dimensionality of the subspace spanned by the components is, in principle, bounded by a modest number of observable metabolites. Secondly, we assume that local susceptibility effects represent the primary sources of signal corruption that tend to disallow such representations. Finally, we assert that the spatial components belong to a class of real-valued, non-negative, and piecewise linear functions, compelled in part through the use of a total variation regularization penalty. After demonstrating superior spatial and spectral localization properties in both numerical and physical phantom data when compared against standard Fourier methods, we proceed to evaluate reconstruction performance in typical in vivo settings, whereby the method is extended in order to promote the recovery of signal variations throughout the MRSI slice thickness. Aside from the various technical obstacles, one of the cardinal prospective challenges for high-resolution MRSI reconstruction is the shortfall of reliable ground truth data prudent for validation, thereby prompting reservations surrounding the resulting experimental outcomes. [...

Structured Sub-Nyquist Sampling with Applications in Compressive Toeplitz Covariance Estimation, Super-Resolution and Phase Retrieval

Sub-Nyquist sampling has received a huge amount of interest in the past decade. In classical compressed sensing theory, if the measurement procedure satisfies a particular condition known as Restricted Isometry Property (RIP), we can achieve stable recovery of signals of low-dimensional intrinsic structures with an order-wise optimal sample size. Such low-dimensional structures include sparse and low rank for both vector and matrix cases. The main drawback of conventional compressed sensing theory is that random measurements are required to ensure the RIP property. However, in many applications such as imaging and array signal processing, applying independent random measurements may not be practical as the systems are deterministic. Moreover, random measurements based compressed sensing always exploits convex programs for signal recovery even in the noiseless case, and solving those programs is computationally intensive if the ambient dimension is large, especially in the matrix case. The main contribution of this dissertation is that we propose a deterministic sub-Nyquist sampling framework for compressing the structured signal and come up with computationally efficient algorithms. Besides widely studied sparse and low-rank structures, we particularly focus on the cases that the signals of interest are stationary or the measurements are of Fourier type. The key difference between our work from classical compressed sensing theory is that we explicitly exploit the second-order statistics of the signals, and study the equivalent quadratic measurement model in the correlation domain. The essential observation made in this dissertation is that a difference/sum coarray structure will arise from the quadratic model if the measurements are of Fourier type. With these observations, we are able to achieve a better compression rate for covariance estimation, identify more sources in array signal processing or recover the signals of larger sparsity. In this dissertation, we will first study the problem of Toeplitz covariance estimation. In particular, we will show how to achieve an order-wise optimal compression rate using the idea of sparse arrays in both general and low-rank cases. Then, an analysis framework of super-resolution with positivity constraint is established. We will present fundamental robustness guarantees, efficient algorithms and applications in practices. Next, we will study the problem of phase-retrieval for which we successfully apply the sparse array ideas by fully exploiting the quadratic measurement model. We achieve near-optimal sample complexity for both sparse and general cases with practical Fourier measurements and provide efficient and deterministic recovery algorithms. In the end, we will further elaborate on the essential role of non-negative constraint in underdetermined inverse problems. In particular, we will analyze the nonlinear co-array interpolation problem and develop a universal upper bound of the interpolation error. Bilinear problem with non-negative constraint will be considered next and the exact characterization of the ambiguous solutions will be established for the first time in literature. At last, we will show how to apply the nested array idea to solve real problems such as Kriging. Using spatial correlation information, we are able to have a stable estimate of the field of interest with fewer sensors than classic methodologies. Extensive numerical experiments are implemented to demonstrate our theoretical claims