Fast Mojette Transform for Discrete Tomography

A new algorithm for reconstructing a two dimensional object from a set of one dimensional projected views is presented that is both computationally exact and experimentally practical. The algorithm has a computational complexity of O(n log2 n) with n = N^2 for an NxN image, is robust in the presence of noise and produces no artefacts in the reconstruction process, as is the case with conventional tomographic methods. The reconstruction process is approximation free because the object is assumed to be discrete and utilizes fully discrete Radon transforms. Noise in the projection data can be suppressed further by introducing redundancy in the reconstruction. The number of projections required for exact reconstruction and the response to noise can be controlled without comprising the digital nature of the algorithm. The digital projections are those of the Mojette Transform, a form of discrete linogram. A simple analytical mapping is developed that compacts these projections exactly into symmetric periodic slices within the Discrete Fourier Transform. A new digital angle set is constructed that allows the periodic slices to completely fill all of the objects Discrete Fourier space. Techniques are proposed to acquire these digital projections experimentally to enable fast and robust two dimensional reconstructions.Comment: 22 pages, 13 figures, Submitted to Elsevier Signal Processin

Recovering missing slices of the discrete fourier transform using ghosts

The discrete Fourier transform (DFT) underpins the solution to many inverse problems commonly possessing missing or unmeasured frequency information. This incomplete coverage of the Fourier space always produces systematic artifacts called Ghosts. In this paper, a fast and exact method for deconvolving cyclic artifacts caused by missing slices of the DFT using redundant image regions is presented. The slices discussed here originate from the exact partitioning of the Discrete Fourier Transform (DFT) space, under the projective Discrete Radon Transform, called the discrete Fourier slice theorem. The method has a computational complexity of O(n\log-{2}n) (for an n=N\times N image) and is constructed from a new cyclic theory of Ghosts. This theory is also shown to unify several aspects of work done on Ghosts over the past three decades. This paper concludes with an application to fast, exact, non-iterative image reconstruction from a highly asymmetric set of rational angle projections that give rise to sets of sparse slices within the DFT

The finite ridgelet transform for image representation

The ridgelet transform (Candès and Donoho, 1999) was introduced as a sparse expansion for functions on continuous spaces that are smooth away from discontinuities along lines. In this paper, we propose an or- thonormal version of the ridgelet transform for discrete and fi- nite-size images. Our construction uses the finite Radon transform (FRAT) (Bolker, 1987:Matùs and Flusser, 1993) as a building block. To overcome the periodiza- tion effect of a finite transform, we introduce a novel ordering of the FRAT coefficients. We also analyze the FRAT as a frame operator and derive the exact frame bounds. The resulting finite ridgelet transform (FRIT) is invertible, nonredundant and computed via fast algorithms. Furthermore, this construction leads to a family of directional and orthonormal bases for images. Numerical results show that the FRIT is more effective than the wavelet transform in approximating and denoising images with straight edges

Fast and Scalable Architectures and Algorithms for the Computation of the Forward and Inverse Discrete Periodic Radon Transform with Applications to 2D Convolutions and Cross-Correlations

The Discrete Radon Transform (DRT) is an essential component of a wide range of applications in image processing, e.g. image denoising, image restoration, texture analysis, line detection, encryption, compressive sensing and reconstructing objects from projections in computed tomography and magnetic resonance imaging. A popular method to obtain the DRT, or its inverse, involves the use of the Fast Fourier Transform, with the inherent approximation/rounding errors and increased hardware complexity due the need for floating point arithmetic implementations. An alternative implementation of the DRT is through the use of the Discrete Periodic Radon Transform (DPRT). The DPRT also exhibits discrete properties of the continuous-space Radon Transform, including the Fourier Slice Theorem and the convolution property. Unfortunately, the use of the DPRT has been limited by the need to compute a large number of additions O(N^3) and the need for a large number of memory accesses. This PhD dissertation introduces a fast and scalable approach for computing the forward and inverse DPRT that is based on the use of: (i) a parallel array of fixed-point adder trees, (ii) circular shift registers to remove the need for accessing external memory components when selecting the input data for the adder trees, and (iii) an image block-based approach to DPRT computation that can fit the proposed architecture to available resources, and as a result, for an NxN image (N prime), the proposed approach can compute up to N^2 additions per clock cycle. Compared to previous approaches, the scalable approach provides the fastest known implementations for different amounts of computational resources. For the fastest case, I introduce optimized architectures that can compute the DPRT and its inverse in just 2N +ceil(log2 N)+1 and 2N +3(log2 N)+B+2 clock cycles respectively, where B is the number of bits used to represent each input pixel. In comparison, the prior state of the art method required N^2 +N +1 clock cycles for computing the forward DPRT. For systems with limited resources, the resource usage can be reduced to O(N) with a running time of ceil(N/2)(N + 9) + N + 2 for the forward DPRT and ceil(N/2)(N + 2) + 3ceil(log2 N) + B + 4 for the inverse. The results also have important applications in the computation of fast convolutions and cross-correlations for large and non-separable kernels. For this purpose, I introduce fast algorithms and scalable architectures to compute 2-D Linear convolutions/cross-correlations using the convolution property of the DPRT and fixed point arithmetic to simplify the 2-D problem into a 1-D problem. Also an alternative system is proposed for non-separable kernels with low rank using the LU decomposition. As a result, for implementations with enough resources, for a an image and convolution kernel of size PxP, linear convolutions/cross correlations can be computed in just 6N + 4 log2 N + 17 clock cycles for N = 2P-1. Finally, I also propose parallel algorithms to compute the forward and inverse DPRT using Graphic Processing Units (GPUs) and CPUs with multiple cores. The proposed algorithms are implemented in a GPU Nvidia Maxwell GM204 with 2048 cores@1367MHz, 348KB L1 cache (24KB per multiprocessor), 2048KB L2 cache (512KB per memory controller), 4GB device memory, and compared against a serial implementation on a CPU Intel Xeon E5-2630 with 8 physical cores (16 logical processors via hyper-threading)@3.2GHz, L1 cache 512K (32KB Instruction cache, 32KB data cache, per core), L2 cache 2MB (256KB per core), L3 cache 20MB (Shared among all cores), 32GB of system memory. For the CPU, there is a tenfold speedup using 16 logical cores versus a single-core serial implementation. For the GPU, there is a 715-fold speedup compared to the serial implementation. For real-time applications, for an 1021x1021 image, the forward DPRT takes 11.5ms and 11.4ms for the inverse

Doctor of Philosophy

dissertationIn Chapter 1, an introduction to basic principles or MRI is given, including the physical principles, basic pulse sequences, and basic hardware. Following the introduction, five different published and yet unpublished papers for improving the utility of MRI are shown. Chapter 2 discusses a small rodent imaging system that was developed for a clinical 3 T MRI scanner. The system integrated specialized radiofrequency (RF) coils with an insertable gradient, enabling 100 'm isotropic resolution imaging of the guinea pig cochlea in vivo, doubling the body gradient strength, slew rate, and contrast-to-noise ratio, and resulting in twice the signal-to-noise (SNR) when compared to the smallest conforming birdcage. Chapter 3 discusses a system using BOLD MRI to measure T2* and invasive fiberoptic probes to measure renal oxygenation (pO2). The significance of this experiment is that it demonstrated previously unknown physiological effects on pO2, such as breath-holds that had an immediate (<1 sec) pO2 decrease (~6 mmHg), and bladder pressure that had pO2 increases (~6 mmHg). Chapter 4 determined the correlation between indicators of renal health and renal fat content. The R2 correlation between renal fat content and eGFR, serum cystatin C, urine protein, and BMI was less than 0.03, with a sample size of ~100 subjects, suggesting that renal fat content will not be a useful indicator of renal health. Chapter 5 is a hardware and pulse sequence technique for acquiring multinuclear 1H and 23Na data within the same pulse sequence. Our system demonstrated a very simple, inexpensive solution to SMI and acquired both nuclei on two 23Na channels using external modifications, and is the first demonstration of radially acquired SMI. Chapter 6 discusses a composite sodium and proton breast array that demonstrated a 2-5x improvement in sodium SNR and similar proton SNR when compared to a large coil with a linear sodium and linear proton channel. This coil is unique in that sodium receive loops are typically built with at least twice the diameter so that they do not have similar SNR increases. The final chapter summarizes the previous chapters