Hammad Omer

A modified POCS‐based reconstruction method for compressively sampled MR imaging

One of the challenging tasks in the application of compressed sensing to magnetic resonance imaging is the reconstruction algorithm that can faithfully recover the MR image from randomly undersampled k‐space data. The nonlinear recovery algorithms based on iterative shrinkage start with a single initial guess and use soft‐thresholding to recover the original MR image from the partial Fourier data. This article presents a novel method based on projection onto convex set (POCS) algorithm but it takes two images and then randomly combines them at each iteration to estimate the original MR image. The performance of the proposed method is validated using the original data taken from the MRI scanner at St. Marys Hospital, London. The experimental results show that the proposed method can reconstruct the original MR image from variable density undersampling scheme in less number of iterations and exhibits better performance in terms of improved signal‐to‐noise ratio, artifact power, and correlation as compared to the reconstruction through low‐resolution and POCS algorithms.

FPGA implementation of real-time SENSE reconstruction using pre-scan and Emaps sensitivities

Sensitivity Encoding (SENSE) is a widely used technique in Parallel Magnetic Resonance Imaging (MRI) to reduce scan time. Reconfigurable hardware based architecture for SENSE can potentially provide image reconstruction with much less computation time. Application specific hardware platform for SENSE may dramatically increase the power efficiency of the system and can decrease the execution time to obtain MR images. A new implementation of SENSE on Field Programmable Gate Array (FPGA) is presented in this study, which provides real-time SENSE reconstruction right on the receiver coil data acquisition system with no need to transfer the raw data to the MRI server, thereby minimizing the transmission noise and memory usage. The proposed SENSE architecture can reconstruct MR images using receiver coil sensitivity maps obtained using pre-scan and eigenvector (E-maps) methods. The results show that the proposed system consumes remarkably less computation time for SENSE reconstruction, i.e., 0.164ms @ 200MHz, while maintaining the quality of the reconstructed images with good mean SNR (29+ dB), less RMSE (<5×10-2) and comparable artefact power (<9×10-4) to conventional SENSE reconstruction. A comparison of the center line profiles of the reconstructed and reference images also indicates a good quality of the reconstructed images. Furthermore, the results indicate that the proposed architectural design can prove to be a significant tool for SENSE reconstruction in modern MRI scanners and its low power consumption feature can be remarkable for portable MRI scanners.

Compressively Sampled MR Image Reconstruction using Generalized Thresholding Iterative Algorithm

Compressed sensing (CS) is an emerging area of interest in Magnetic Resonance Imaging (MRI). CS is used for the reconstruction of the images from a very limited number of samples in k-space. This significantly reduces the MRI data acquisition time. One important requirement for signal recovery in CS is the use of an appropriate non-linear reconstruction algorithm. It is a challenging task to choose a reconstruction algorithm that would accurately reconstruct the MR images from the under-sampled k-space data. Various algorithms have been used to solve the system of non-linear equations for better image quality and reconstruction speed in CS. In the recent past, iterative soft thresholding algorithm (ISTA) has been introduced in CS-MRI. This algorithm directly cancels the incoherent artifacts produced because of the undersampling in k-space. This paper introduces an improved iterative algorithm based on p-thresholding technique for CS-MRI image reconstruction. The use of p-thresholding function promotes sparsity in the image which is a key factor for CS based image reconstruction. The p-thresholding based iterative algorithm is a modification of ISTA, and minimizes non-convex functions. It has been shown that the proposed p-thresholding iterative algorithm can be used effectively to recover fully sampled image from the under-sampled data in MRI. The performance of the proposed method is verified using simulated and actual MRI data taken at St. Marys Hospital, London. The quality of the reconstructed images is measured in terms of peak signal-to-noise ratio (PSNR), artifact power (AP), and structural similarity index measure (SSIM). The proposed approach shows improved performance when compared to other iterative algorithms based on log thresholding, soft thresholding and hard thresholding techniques at different reduction factors.

Iterative Schemes to Solve Low-Dimensional Calibration Equations in Parallel MR Image Reconstruction with GRAPPA

GRAPPA (Generalized Autocalibrating Partially Parallel Acquisition) is a widely used parallel MRI reconstruction technique. The processing of data from multichannel receiver coils may increase the storage and computational requirements of GRAPPA reconstruction. Random projection on GRAPPA (RP-GRAPPA) uses random projection (RP) method to overcome the computational overheads of solving large linear equations in the calibration phase of GRAPPA, saving reconstruction time. However, RP-GRAPPA compromises the reconstruction accuracy in case of large reductions in the dimensions of calibration equations. In this paper, we present the implementation of GRAPPA reconstruction method using potential iterative solvers to estimate the reconstruction coefficients from the randomly projected calibration equations. Experimental results show that the proposed methods withstand the reconstruction accuracy (visually and quantitatively) against large reductions in the dimension of linear equations, when compared with RP-GRAPPA reconstruction. Particularly, the proposed method using conjugate gradient for least squares (CGLS) demonstrates more savings in the computational time of GRAPPA, without significant loss in the reconstruction accuracy, when compared with RP-GRAPPA. It is also demonstrated that the proposed method using CGLS complements the channel compression method for reducing the computational complexities associated with higher channel count, thereby resulting in additional memory savings and speedup.

QR-decomposition based SENSE reconstruction using parallel architecture

Magnetic Resonance Imaging (MRI) is a powerful medical imaging technique that provides essential clinical information about the human body. One major limitation of MRI is its long scan time. Implementation of advance MRI algorithms on a parallel architecture (to exploit inherent parallelism) has a great potential to reduce the scan time. Sensitivity Encoding (SENSE) is a Parallel Magnetic Resonance Imaging (pMRI) algorithm that utilizes receiver coil sensitivities to reconstruct MR images from the acquired under-sampled k-space data. At the heart of SENSE lies inversion of a rectangular encoding matrix. This work presents a novel implementation of GPU based SENSE algorithm, which employs QR decomposition for the inversion of the rectangular encoding matrix. For a fair comparison, the performance of the proposed GPU based SENSE reconstruction is evaluated against single and multicore CPU using openMP. Several experiments against various acceleration factors (AFs) are performed using multichannel (8, 12 and 30) phantom and in-vivo human head and cardiac datasets. Experimental results show that GPU significantly reduces the computation time of SENSE reconstruction as compared to multi-core CPU (approximately 12x speedup) and single-core CPU (approximately 53x speedup) without any degradation in the quality of the reconstructed images.

A high-resolution reconfigurable sigma-delta Digital-to-Analog Converter for RF pulse transmission in MRI scanners

In Magnetic Resonance Imaging (MRI) scanners Radio Frequency (RF) signals are important to accurately excite target tissues. RF signals depend on Digital-to-Analog Converters (DAC) output which depends on sequence numbers issued from control room. This paper presents a sigma-delta modulator (SDM), followed by a DAC architecture that can be reconfigured while an MRI scanner is operating and pipelining is not required. The reconfigurable SDM is implemented in a 65nm CMOS technology and operates at an oversampling ratio (OSR) of 64 times. The modulator clocks at 2 GHz frequency with a 1.2-V supply voltage. The modulator occupies an area of 29 × 32 sq μm and consumes 319.1 mW. The proposed SDM-DAC is well-suited for the RF transmitter in the MRI scanner. The reconfigurability feature allows to select different resolutions for various types of RF pulses and can thereby target specific tissues more accurately. 1

Modified POCS Based Reconstruction for Compressed Sensing in MRI

Compressed Sensing usage in Magnetic Resonance Imaging greatly enhances the utility and effectiveness of the data acquisition process. Magnetic resonance images can be safely reconstructed from the sparse randomly under-sampled data, using a non-linear recovery technique. There are several reconstruction algorithms used in Compressed Sensing to obtain a Magnetic resonance image from highly under-sampled data e.g. conjugate gradient, separable surrogate function, projection on convex sets and many more. This research work aim store view some of these Compressed Sensing reconstruction algorithms, analyze and evaluate their performance and to propose a similar technique that satisfies the requirements of Compressed Sensing and outperforms the methods already in use. A modified Projection over convex set technique has been proposed which involves the application of discrete cosine transform to standard algorithm. The proposed technique is evaluated using the actual data obtained from the Magnetic resonance imaging scanner at St. Marys Hospital London. It can be concluded from the results that the proposed method exhibits better performance in terms of improved artifact power, signal-to-noise ratio and is computationally less intensive as compared to other reconstruction algorithms.