Accelerated Cardiovascular Magnetic Resonance Imaging Using Radial Acquisition with Compressed Sensing

Magnetic resonance imaging (MRI) is a medical imaging technique that can visualize internal organs for examination and diagnosis. It is non-invasive and ionizing radiation-free, and provides good contrast between different soft tissues. One of the drawbacks of MRI is its lengthy acquisition time. Significant research has been done in order to accelerate the MRI data acquisition and reduce the scan time. Compressed sensing (CS) has been recently proposed for accelerating MRI acquisition time. Compressed sensing recovers the desired image from undersampled MRI dataset by exploiting the sparsity of MR image in transform domain. In this thesis, we propose CS reconstruction methods in various cardiovascular MRI applications for accelerated imaging. We consider 3D whole-heart coronary MRI. Isotropic 3D radial trajectories allow undersampling of k-space in all three dimensions, enabling accelerated acquisition of volumetric data. Our CS based approach provides further acceleration by removing undersampling artifacts and improving image quality. However, the underlying heavy computational overhead of this method is also a limiting factor which depreciates the applicability of CS. A parallelized implementation of an iterative CS reconstruction for 3D radial acquisitions using a graphics processing unit is presented to reduce the reconstruction time. The efficacy of CS is also investigated in cardiac cine MRI. Cardiac function is usually assessed using segmented cine acquisition with multiple breath-holds (BHs). Subjects are given resting periods between adjacent BHs, where no data is acquired, resulting in low acquisition efficiency. We propose an accelerated radial acquisition for BH cine imaging which utilizes the resting period to acquire additional free-breathing (FB) data without increasing scan time. The difference image between BH and FB acquisitions is used as the sparsity regularization of the CS reconstruction. Compressed sensing can be used as a respiratory motion correction technique in FB whole-heart MRI. Respiratory motion causes aliasing artifacts and blurring on the resulting image. To obtain motion-free images, a respiratory navigator is often used to track the heart position, but the scan efficiency is reduced to 30-50% resulting in a prolonged scan. We propose a CS reconstruction to correct respiratory motion by using an undersampled dataset which only contains motion-free k-space lines whereas the motion-corrupted lines are excluded from the reconstruction.Engineering and Applied Science

Zero-padding Network Coding and Compressed Sensing for Optimized Packets Transmission

Ubiquitous Internet of Things (IoT) is destined to connect everybody and everything on a never-before-seen scale. Such networks, however, have to tackle the inherent issues created by the presence of very heterogeneous data transmissions over the same shared network. This very diverse communication, in turn, produces network packets of various sizes ranging from very small sensory readings to comparatively humongous video frames. Such a massive amount of data itself, as in the case of sensory networks, is also continuously captured at varying rates and contributes to increasing the load on the network itself, which could hinder transmission efficiency. However, they also open up possibilities to exploit various correlations in the transmitted data due to their sheer number. Reductions based on this also enable the networks to keep up with the new wave of big data-driven communications by simply investing in the promotion of select techniques that efficiently utilize the resources of the communication systems. One of the solutions to tackle the erroneous transmission of data employs linear coding techniques, which are ill-equipped to handle the processing of packets with differing sizes. Random Linear Network Coding (RLNC), for instance, generates unreasonable amounts of padding overhead to compensate for the different message lengths, thereby suppressing the pervasive benefits of the coding itself. We propose a set of approaches that overcome such issues, while also reducing the decoding delays at the same time. Specifically, we introduce and elaborate on the concept of macro-symbols and the design of different coding schemes. Due to the heterogeneity of the packet sizes, our progressive shortening scheme is the first RLNC-based approach that generates and recodes unequal-sized coded packets. Another of our solutions is deterministic shifting that reduces the overall number of transmitted packets. Moreover, the RaSOR scheme employs coding using XORing operations on shifted packets, without the need for coding coefficients, thus favoring linear encoding and decoding complexities. Another facet of IoT applications can be found in sensory data known to be highly correlated, where compressed sensing is a potential approach to reduce the overall transmissions. In such scenarios, network coding can also help. Our proposed joint compressed sensing and real network coding design fully exploit the correlations in cluster-based wireless sensor networks, such as the ones advocated by Industry 4.0. This design focused on performing one-step decoding to reduce the computational complexities and delays of the reconstruction process at the receiver and investigates the effectiveness of combined compressed sensing and network coding

Profile-driven parallelisation of sequential programs

Traditional parallelism detection in compilers is performed by means of static analysis and more specifically data and control dependence analysis. The information that is available at compile time, however, is inherently limited and therefore restricts the parallelisation opportunities. Furthermore, applications written in C – which represent the majority of today’s scientific, embedded and system software – utilise many lowlevel features and an intricate programming style that forces the compiler to even more conservative assumptions. Despite the numerous proposals to handle this uncertainty at compile time using speculative optimisation and parallelisation, the software industry still lacks any pragmatic approaches that extracts coarse-grain parallelism to exploit the multiple processing units of modern commodity hardware. This thesis introduces a novel approach for extracting and exploiting multiple forms of coarse-grain parallelism from sequential applications written in C. We utilise profiling information to overcome the limitations of static data and control-flow analysis enabling more aggressive parallelisation. Profiling is performed using an instrumentation scheme operating at the Intermediate Representation (Ir) level of the compiler. In contrast to existing approaches that depend on low-level binary tools and debugging information, Ir-profiling provides precise and direct correlation of profiling information back to the Ir structures of the compiler. Additionally, our approach is orthogonal to existing automatic parallelisation approaches and additional fine-grain parallelism may be exploited. We demonstrate the applicability and versatility of the proposed methodology using two studies that target different forms of parallelism. First, we focus on the exploitation of loop-level parallelism that is abundant in many scientific and embedded applications. We evaluate our parallelisation strategy against the Nas and Spec Fp benchmarks and two different multi-core platforms (a shared-memory Intel Xeon Smp and a heterogeneous distributed-memory Ibm Cell blade). Empirical evaluation shows that our approach not only yields significant improvements when compared with state-of- the-art parallelising compilers, but comes close to and sometimes exceeds the performance of manually parallelised codes. On average, our methodology achieves 96% of the performance of the hand-tuned parallel benchmarks on the Intel Xeon platform, and a significant speedup for the Cell platform. The second study, addresses the problem of partially sequential loops, typically found in implementations of multimedia codecs. We develop a more powerful whole-program representation based on the Program Dependence Graph (Pdg) that supports profiling, partitioning and codegeneration for pipeline parallelism. In addition we demonstrate how this enhances conventional pipeline parallelisation by incorporating support for multi-level loops and pipeline stage replication in a uniform and automatic way. Experimental results using a set of complex multimedia and stream processing benchmarks confirm the effectiveness of the proposed methodology that yields speedups up to 4.7 on a eight-core Intel Xeon machine

High-Performance Modelling and Simulation for Big Data Applications

This open access book was prepared as a Final Publication of the COST Action IC1406 “High-Performance Modelling and Simulation for Big Data Applications (cHiPSet)“ project. Long considered important pillars of the scientific method, Modelling and Simulation have evolved from traditional discrete numerical methods to complex data-intensive continuous analytical optimisations. Resolution, scale, and accuracy have become essential to predict and analyse natural and complex systems in science and engineering. When their level of abstraction raises to have a better discernment of the domain at hand, their representation gets increasingly demanding for computational and data resources. On the other hand, High Performance Computing typically entails the effective use of parallel and distributed processing units coupled with efficient storage, communication and visualisation systems to underpin complex data-intensive applications in distinct scientific and technical domains. It is then arguably required to have a seamless interaction of High Performance Computing with Modelling and Simulation in order to store, compute, analyse, and visualise large data sets in science and engineering. Funded by the European Commission, cHiPSet has provided a dynamic trans-European forum for their members and distinguished guests to openly discuss novel perspectives and topics of interests for these two communities. This cHiPSet compendium presents a set of selected case studies related to healthcare, biological data, computational advertising, multimedia, finance, bioinformatics, and telecommunications

High-Performance Modelling and Simulation for Big Data Applications

This open access book was prepared as a Final Publication of the COST Action IC1406 “High-Performance Modelling and Simulation for Big Data Applications (cHiPSet)“ project. Long considered important pillars of the scientific method, Modelling and Simulation have evolved from traditional discrete numerical methods to complex data-intensive continuous analytical optimisations. Resolution, scale, and accuracy have become essential to predict and analyse natural and complex systems in science and engineering. When their level of abstraction raises to have a better discernment of the domain at hand, their representation gets increasingly demanding for computational and data resources. On the other hand, High Performance Computing typically entails the effective use of parallel and distributed processing units coupled with efficient storage, communication and visualisation systems to underpin complex data-intensive applications in distinct scientific and technical domains. It is then arguably required to have a seamless interaction of High Performance Computing with Modelling and Simulation in order to store, compute, analyse, and visualise large data sets in science and engineering. Funded by the European Commission, cHiPSet has provided a dynamic trans-European forum for their members and distinguished guests to openly discuss novel perspectives and topics of interests for these two communities. This cHiPSet compendium presents a set of selected case studies related to healthcare, biological data, computational advertising, multimedia, finance, bioinformatics, and telecommunications

A comparison of the CAR and DAGAR spatial random effects models with an application to diabetics rate estimation in Belgium

When hierarchically modelling an epidemiological phenomenon on a finite collection of sites in space, one must always take a latent spatial effect into account in order to capture the correlation structure that links the phenomenon to the territory. In this work, we compare two autoregressive spatial models that can be used for this purpose: the classical CAR model and the more recent DAGAR model. Differently from the former, the latter has a desirable property: its ρ parameter can be naturally interpreted as the average neighbor pair correlation and, in addition, this parameter can be directly estimated when the effect is modelled using a DAGAR rather than a CAR structure. As an application, we model the diabetics rate in Belgium in 2014 and show the adequacy of these models in predicting the response variable when no covariates are available

A Statistical Approach to the Alignment of fMRI Data

Multi-subject functional Magnetic Resonance Image studies are critical. The anatomical and functional structure varies across subjects, so the image alignment is necessary. We define a probabilistic model to describe functional alignment. Imposing a prior distribution, as the matrix Fisher Von Mises distribution, of the orthogonal transformation parameter, the anatomical information is embedded in the estimation of the parameters, i.e., penalizing the combination of spatially distant voxels. Real applications show an improvement in the classification and interpretability of the results compared to various functional alignment methods