Towards Fast and High-quality Biomedical Image Reconstruction

Department of Computer Science and EngineeringReconstruction is an important module in the image analysis pipeline with purposes of isolating the majority of meaningful information that hidden inside the acquired data. The term ???reconstruction??? can be understood and subdivided in several specific tasks in different modalities. For example, in biomedical imaging, such as Computed Tomography (CT), Magnetic Resonance Image (MRI), that term stands for the transformation from the, possibly fully or under-sampled, spectral domains (sinogram for CT and k-space for MRI) to the visible image domains. Or, in connectomics, people usually refer it to segmentation (reconstructing the semantic contact between neuronal connections) or denoising (reconstructing the clean image). In this dissertation research, I will describe a set of my contributed algorithms from conventional to state-of-the-art deep learning methods, with a transition at the data-driven dictionary learning approaches that tackle the reconstruction problems in various image analysis tasks.clos

Image Reconstructions of Compressed Sensing MRI with Multichannel Data

Magnetic resonance imaging (MRI) provides high spatial resolution, high-quality of soft-tissue contrast, and multi-dimensional images. However, the speed of data acquisition limits potential applications. Compressed sensing (CS) theory allowing data being sampled at sub-Nyquist rate provides a possibility to accelerate the MRI scan time. Since most MRI scanners are currently equipped with multi-channel receiver systems, integrating CS with multi-channel systems can further shorten the scan time and also provide a better image quality. In this dissertation, we develop several techniques for integrating CS with parallel MRI. First, we propose a method which extends the reweighted l1 minimization to the CS-MRI with multi-channel data. The individual channel images are recovered according to the reweighted l1 minimization algorithm. Then, the final image is combined by the sum-of-squares method. Computer simulations show that the new method can improve the reconstruction quality at a slightly increased computation cost. Second, we propose a reconstruction approach using the ubiquitously available multi-core CPU to accelerate CS reconstructions of multiple channel data. CS reconstructions for phase array system using iterative l1 minimization are significantly time-consuming, where the computation complexity scales with the number of channels. The experimental results show that the reconstruction efficiency benefits significantly from parallelizing the CS reconstructions, and pipelining multi-channel data on multi-core processors. In our experiments, an additional speedup factor of 1.6 to 2.0 was achieved using the proposed method on a quad-core CPU. Finally, we present an efficient reconstruction method for high-dimensional CS MRI with a GPU platform to shorten the time of iterative computations. Data managements as well as the iterative algorithm are properly designed to meet the way of SIMD (single instruction/multiple data) parallelizations. For three-dimension multi-channel data, all slices along frequency encoding direction and multiple channels are highly parallelized and simultaneously processed within GPU. Generally, the runtime on GPU only requires 2.3 seconds for reconstructing a simulated 4-channel data with a volume size of 256×256×32. Comparing to 67 seconds using CPU, it achieves 28 faster with the proposed method. The rapid reconstruction algorithms demonstrated in this work are expected to help bring high dimensional, multichannel parallel CS MRI closer to clinical applications

Improved 3D MR Image Acquisition and Processing in Congenital Heart Disease

Congenital heart disease (CHD) is the most common type of birth defect, affecting about 1% of the population. MRI is an essential tool in the assessment of CHD, including diagnosis, intervention planning and follow-up. Three-dimensional MRI can provide particularly rich visualization and information. However, it is often complicated by long scan times, cardiorespiratory motion, injection of contrast agents, and complex and time-consuming postprocessing. This thesis comprises four pieces of work that attempt to respond to some of these challenges. The first piece of work aims to enable fast acquisition of 3D time-resolved cardiac imaging during free breathing. Rapid imaging was achieved using an efficient spiral sequence and a sparse parallel imaging reconstruction. The feasibility of this approach was demonstrated on a population of 10 patients with CHD, and areas of improvement were identified. The second piece of work is an integrated software tool designed to simplify and accelerate the development of machine learning (ML) applications in MRI research. It also exploits the strengths of recently developed ML libraries for efficient MR image reconstruction and processing. The third piece of work aims to reduce contrast dose in contrast-enhanced MR angiography (MRA). This would reduce risks and costs associated with contrast agents. A deep learning-based contrast enhancement technique was developed and shown to improve image quality in real low-dose MRA in a population of 40 children and adults with CHD. The fourth and final piece of work aims to simplify the creation of computational models for hemodynamic assessment of the great arteries. A deep learning technique for 3D segmentation of the aorta and the pulmonary arteries was developed and shown to enable accurate calculation of clinically relevant biomarkers in a population of 10 patients with CHD

Novel high performance techniques for high definition computer aided tomography

Mención Internacional en el título de doctorMedical image processing is an interdisciplinary field in which multiple research areas are involved: image acquisition, scanner design, image reconstruction algorithms, visualization, etc. X-Ray Computed Tomography (CT) is a medical imaging modality based on the attenuation suffered by the X-rays as they pass through the body. Intrinsic differences in attenuation properties of bone, air, and soft tissue result in high-contrast images of anatomical structures. The main objective of CT is to obtain tomographic images from radiographs acquired using X-Ray scanners. The process of building a 3D image or volume from the 2D radiographs is known as reconstruction. One of the latest trends in CT is the reduction of the radiation dose delivered to patients through the decrease of the amount of acquired data. This reduction results in artefacts in the final images if conventional reconstruction methods are used, making it advisable to employ iterative reconstruction algorithms. There are numerous reconstruction algorithms available, from which we can highlight two specific types: traditional algorithms, which are fast but do not enable the obtaining of high quality images in situations of limited data; and iterative algorithms, slower but more reliable when traditional methods do not reach the quality standard requirements. One of the priorities of reconstruction is the obtaining of the final images in near real time, in order to reduce the time spent in diagnosis. To accomplish this objective, new high performance techniques and methods for accelerating these types of algorithms are needed. This thesis addresses the challenges of both traditional and iterative reconstruction algorithms, regarding acceleration and image quality. One common approach for accelerating these algorithms is the usage of shared-memory and heterogeneous architectures. In this thesis, we propose a novel simulation/reconstruction framework, namely FUX-Sim. This framework follows the hypothesis that the development of new flexible X-ray systems can benefit from computer simulations, which may also enable performance to be checked before expensive real systems are implemented. Its modular design abstracts the complexities of programming for accelerated devices to facilitate the development and evaluation of the different configurations and geometries available. In order to obtain near real execution times, low-level optimizations for the main components of the framework are provided for Graphics Processing Unit (GPU) architectures. Other alternative tackled in this thesis is the acceleration of iterative reconstruction algorithms by using distributed memory architectures. We present a novel architecture that unifies the two most important computing paradigms for scientific computing nowadays: High Performance Computing (HPC). The proposed architecture combines Big Data frameworks with the advantages of accelerated computing. The proposed methods presented in this thesis provide more flexible scanner configurations as they offer an accelerated solution. Regarding performance, our approach is as competitive as the solutions found in the literature. Additionally, we demonstrate that our solution scales with the size of the problem, enabling the reconstruction of high resolution images.El procesamiento de imágenes médicas es un campo interdisciplinario en el que participan múltiples áreas de investigación como la adquisición de imágenes, diseño de escáneres, algoritmos de reconstrucción de imágenes, visualización, etc. La tomografía computarizada (TC) de rayos X es una modalidad de imágen médica basada en el cálculo de la atenuación sufrida por los rayos X a medida que pasan por el cuerpo a escanear. Las diferencias intrínsecas en la atenuación de hueso, aire y tejido blando dan como resultado imágenes de alto contraste de estas estructuras anatómicas. El objetivo principal de la TC es obtener imágenes tomográficas a partir estas radiografías obtenidas mediante escáneres de rayos X. El proceso de construir una imagen o volumen en 3D a partir de las radiografías 2D se conoce como reconstrucción. Una de las últimas tendencias en la tomografía computarizada es la reducción de la dosis de radiación administrada a los pacientes a través de la reducción de la cantidad de datos adquiridos. Esta reducción da como resultado artefactos en las imágenes finales si se utilizan métodos de reconstrucción convencionales, por lo que es aconsejable emplear algoritmos de reconstrucción iterativos. Existen numerosos algoritmos de reconstrucción disponibles a partir de los cuales podemos destacar dos categorías: algoritmos tradicionales, rápidos pero no permiten obtener imágenes de alta calidad en situaciones en las que los datos son limitados; y algoritmos iterativos, más lentos pero más estables en situaciones donde los métodos tradicionales no alcanzan los requisitos en cuanto a la calidad de la imagen. Una de las prioridades de la reconstrucción es la obtención de las imágenes finales en tiempo casi real, con el fin de reducir el tiempo de diagnóstico. Para lograr este objetivo, se necesitan nuevas técnicas y métodos de alto rendimiento para acelerar estos algoritmos. Esta tesis aborda los desafíos de los algoritmos de reconstrucción tradicionales e iterativos, con respecto a la aceleración y la calidad de imagen. Un enfoque común para acelerar estos algoritmos es el uso de arquitecturas de memoria compartida y heterogéneas. En esta tesis, proponemos un nuevo sistema de simulación/reconstrucción, llamado FUX-Sim. Este sistema se construye alrededor de la hipótesis de que el desarrollo de nuevos sistemas de rayos X flexibles puede beneficiarse de las simulaciones por computador, en los que también se puede realizar un control del rendimiento de los nuevos sistemas a desarrollar antes de su implementación física. Su diseño modular abstrae las complejidades de la programación para aceleradores con el objetivo de facilitar el desarrollo y la evaluación de las diferentes configuraciones y geometrías disponibles. Para obtener ejecuciones en casi tiempo real, se proporcionan optimizaciones de bajo nivel para los componentes principales del sistema en las arquitecturas GPU. Otra alternativa abordada en esta tesis es la aceleración de los algoritmos de reconstrucción iterativa mediante el uso de arquitecturas de memoria distribuidas. Presentamos una arquitectura novedosa que unifica los dos paradigmas informáticos más importantes en la actualidad: computación de alto rendimiento (HPC) y Big Data. La arquitectura propuesta combina sistemas Big Data con las ventajas de los dispositivos aceleradores. Los métodos propuestos presentados en esta tesis proporcionan configuraciones de escáner más flexibles y ofrecen una solución acelerada. En cuanto al rendimiento, nuestro enfoque es tan competitivo como las soluciones encontradas en la literatura. Además, demostramos que nuestra solución escala con el tamaño del problema, lo que permite la reconstrucción de imágenes de alta resolución.This work has been mainly funded thanks to a FPU fellowship (FPU14/03875) from the Spanish Ministry of Education. It has also been partially supported by other grants: • DPI2016-79075-R. “Nuevos escenarios de tomografía por rayos X”, from the Spanish Ministry of Economy and Competitiveness. • TIN2016-79637-P Towards unification of HPC and Big Data Paradigms from the Spanish Ministry of Economy and Competitiveness. • Short-term scientific missions (STSM) grant from NESUS COST Action IC1305. • TIN2013-41350-P, Scalable Data Management Techniques for High-End Computing Systems from the Spanish Ministry of Economy and Competitiveness. • RTC-2014-3028-1 NECRA Nuevos escenarios clinicos con radiología avanzada from the Spanish Ministry of Economy and Competitiveness.Programa Oficial de Doctorado en Ciencia y Tecnología InformáticaPresidente: José Daniel García Sánchez.- Secretario: Katzlin Olcoz Herrero.- Vocal: Domenico Tali