Parallel Computation of Nonrigid Image Registration

Automatic intensity-based nonrigid image registration brings significant impact in medical applications such as multimodality fusion of images, serial comparison for monitoring disease progression or regression, and minimally invasive image-guided interventions. However, due to memory and compute intensive nature of the operations, intensity-based image registration has remained too slow to be practical for clinical adoption, with its use limited primarily to as a pre-operative too. Efficient registration methods can lead to new possibilities for development of improved and interactive intraoperative tools and capabilities. In this thesis, we propose an efficient parallel implementation for intensity-based three-dimensional nonrigid image registration on a commodity graphics processing unit. Optimization techniques are developed to accelerate the compute-intensive mutual information computation. The study is performed on the hierarchical volume subdivision-based algorithm, which is inherently faster than other nonrigid registration algorithms and structurally well-suited for data-parallel computation platforms. The proposed implementation achieves more than 50-fold runtime improvement over a standard implementation on a CPU. The execution time of nonrigid image registration is reduced from hours to minutes while retaining the same level of registration accuracy

Efficient dense non-rigid registration using the free-form deformation framework

Medical image registration consists of finding spatial correspondences between two images or more. It is a powerful tool which is commonly used in various medical image processing tasks. Even though medical image registration has been an active topic of research for the last two decades, significant challenges in the field remain to be solved. This thesis addresses some of these challenges through extensions to the Free-Form Deformation (FFD) registration framework, which is one of the most widely used and well-established non-rigid registration algorithm. Medical image registration is a computationally expensive task because of the high degrees of freedom of the non-rigid transformations. In this work, the FFD algorithm has been re-factored to enable fast processing, while maintaining the accuracy of the results. In addition, parallel computing paradigms have been employed to provide near real-time image registration capabilities. Further modifications have been performed to improve the registration robustness to artifacts such as tissues non-uniformity. The plausibility of the generated deformation field has been improved through the use of bio-mechanical models based regularization. Additionally, diffeomorphic extensions to the algorithm were also developed. The work presented in this thesis has been extensively validated using brain magnetic resonance imaging of patients diagnosed with dementia or patients undergoing brain resection. It has also been applied to lung X-ray computed tomography and imaging of small animals. Alongside with this thesis an open-source package, NiftyReg, has been developed to release the presented work to the medical imaging community

Computación paralela heterogénea en registro de imágenes y aplicaciones de álgebra lineal

This doctoral thesis focuses on GPU acceleration of medical image registration and sparse general matrix-matrix multiplication (SpGEMM). The comprehensive work presented here aims to enable new possibilities in Image Guided Surgery (IGS). IGS provides the surgeon with advanced navigation tools during surgery. Image registration, which is a part of IGS, is computationally demanding, therefore GPU acceleration is greatly desirable. spGEMM, which is an essential part in many scientific and data analytics applications, e.g., graph applications, is also a useful tool in biomechanical modeling and sparse vessel network registration. We present this work in two parts. The first part of this thesis describes the optimization of the most demanding part of non-rigid Free Form Deformation registration, i.e., B-spline interpolation. Our novel optimization technique minimizes the data movement between processing cores and memory and maximizes the utilization of the very fast register file. In addition, our approach re-formulates B-spline interpolation to fully utilize Fused Multiply Accumulation instructions for additional benefits in performance and accuracy. Our optimized B-spline interpolation provides significant speedup to image registration. The second part describes the optimization of spGEMM. Hardware manufacturers, with the aim of increasing the performance of deep-learning, created specialized dense matrix multiplication units, called Tensor Core Units (TCUs). However, until now, no work takes advantage of TCUs for sparse matrix multiplication. With this work we provide the first TCU implementation of spGEMM and prove its benefits over conventional GPU spGEMM.Esta tesis doctoral se centra en la aceleración por GPU del registro de imágenes médicas y la multiplicación de matrices dispersas (SpGEMM). El exhaustivo trabajo presentado aquí tiene como objetivo permitir nuevas posibilidades en la cirugía guiada por imagen (IGS). IGS proporciona al cirujano herramientas de navegación avanzadas durante la cirugía. El registro de imágenes, parte de IGS computacionalmente exigente, por lo tanto, la aceleración en GPU es muy deseable. spGEMM, la cual es una parte esencial en muchas aplicaciones científicas y de análisis de datos, por ejemplo, aplicaciones de gráficos, también es una herramienta útil en el modelado biomecánico y el registro de redes de vasos dispersos. Presentamos este trabajo en dos partes. La primera parte de esta tesis describe la optimización de la parte más exigente del registro de deformación de forma libre no rígida, es decir, la interpolación B-spline. Nuestra novedosa técnica de optimización minimiza el movimiento de datos entre los núcleos de procesamiento y la memoria y maximiza la utilización del archivo de registro rápido. Además, nuestro enfoque reformula la interpolación B-spline para utilizar completamente las instrucciones de multiplicación-acumulación fusionada (FMAC) para obtener beneficios adicionales en rendimiento y precisión. Nuestra interpolación B-spline optimizada proporciona una aceleración significativa en el registro de imágenes. La segunda parte describe la optimización de spGEMM. Los fabricantes de hardware, con el objetivo de aumentar el rendimiento del aprendizaje profundo, crearon unidades especializadas de multiplicación de matrices densas, llamadas Tensor Core Units (TCU). Sin embargo, hasta ahora, no se ha encontrado ningún trabajo aprovecha las TCU para la multiplicación de matrices dispersas. Con este trabajo, proporcionamos la primera implementación TCU de spGEMM y demostramos sus beneficios sobre la spGEMM convencional operada sobre dispositivos GPU

On the Real-Time Performance, Robustness and Accuracy of Medical Image Non-Rigid Registration

Three critical issues about medical image non-rigid registration are performance, robustness and accuracy. A registration method, which is capable of responding timely with an accurate alignment, robust against the variation of the image intensity and the missing data, is desirable for its clinical use. This work addresses all three of these issues. Unacceptable execution time of Non-rigid registration (NRR) often presents a major obstacle to its routine clinical use. We present a hybrid data partitioning method to parallelize a NRR method on a cooperative architecture, which enables us to get closer to the goal: accelerating using architecture rather than designing a parallel algorithm from scratch. to further accelerate the performance for the GPU part, a GPU optimization tool is provided to automatically optimize GPU execution configuration.;Missing data and variation of the intensity are two severe challenges for the robustness of the registration method. A novel point-based NRR method is presented to resolve mapping function (deformation field) with the point correspondence missing. The novelty of this method lies in incorporating a finite element biomechanical model into an Expectation and Maximization (EM) framework to resolve the correspondence and mapping function simultaneously. This method is extended to deal with the deformation induced by tumor resection, which imposes another challenge, i.e. incomplete intra-operative MRI. The registration is formulated as a three variable (Correspondence, Deformation Field, and Resection Region) functional minimization problem and resolved by a Nested Expectation and Maximization framework. The experimental results show the effectiveness of this method in correcting the deformation in the vicinity of the tumor. to deal with the variation of the intensity, two different methods are developed depending on the specific application. For the mono-modality registration on delayed enhanced cardiac MRI and cine MRI, a hybrid registration method is designed by unifying both intensity- and feature point-based metrics into one cost function. The experiment on the moving propagation of suspicious myocardial infarction shows effectiveness of this hybrid method. For the multi-modality registration on MRI and CT, a Mutual Information (MI)-based NRR is developed by modeling the underlying deformation as a Free-Form Deformation (FFD). MI is sensitive to the variation of the intensity due to equidistant bins. We overcome this disadvantage by designing a Top-to-Down K-means clustering method to naturally group similar intensities into one bin. The experiment shows this method can increase the accuracy of the MI-based registration.;In image registration, a finite element biomechanical model is usually employed to simulate the underlying movement of the soft tissue. We develop a multi-tissue mesh generation method to build a heterogeneous biomechanical model to realistically simulate the underlying movement of the brain. We focus on the following four critical mesh properties: tissue-dependent resolution, fidelity to tissue boundaries, smoothness of mesh surfaces, and element quality. Each mesh property can be controlled on a tissue level. The experiments on comparing the homogeneous model with the heterogeneous model demonstrate the effectiveness of the heterogeneous model in improving the registration accuracy

Towards Real-time Remote Processing of Laparoscopic Video

Laparoscopic surgery is a minimally invasive technique where surgeons insert a small video camera into the patient\u27s body to visualize internal organs and use small tools to perform these procedures. However, the benefit of small incisions has a disadvantage of limited visualization of subsurface tissues. Image-guided surgery (IGS) uses pre-operative and intra-operative images to map subsurface structures and can reduce the limitations of laparoscopic surgery. One particular laparoscopic system is the daVinci-si robotic surgical vision system. The video streams generate approximately 360 megabytes of data per second, demonstrating a trend toward increased data sizes in medicine, primarily due to higher-resolution video cameras and imaging equipment. Real-time processing this large stream of data on a bedside PC, single or dual node setup, may be challenging and a high-performance computing (HPC) environment is not typically available at the point of care. To process this data on remote HPC clusters at the typical 30 frames per second rate (fps), it is required that each 11.9 MB (1080p) video frame be processed by a server and returned within the time this frame is displayed or 1/30th of a second. The ability to acquire, process, and visualize data in real time is essential for the performance of complex tasks as well as minimizing risk to the patient. We have implemented and compared performance of compression, segmentation and registration algorithms on Clemson\u27s Palmetto supercomputer using dual Nvidia graphics processing units (GPUs) per node and compute unified device architecture (CUDA) programming model. We developed three separate applications that run simultaneously: video acquisition, image processing, and video display. The image processing application allows several algorithms to run simultaneously on different cluster nodes and transfer images through message passing interface (MPI). Our segmentation and registration algorithms resulted in an acceleration factor of around 2 and 8 times respectively. To achieve a higher frame rate, we also resized images and reduced the overall processing time. As a result, using high-speed network to access computing clusters with GPUs to implement these algorithms in parallel will improve surgical procedures by providing real-time medical image processing and laparoscopic data

Efficient probabilistic and geometric anatomical mapping using particle mesh approximation on GPUs

pre-printDeformable image registration in the presence of considerable contrast differences and large size and shape changes presents significant research challenges. First, it requires a robust registration framework that does not depend on intensity measurements and can handle large nonlinear shape variations. Second, it involves the expensive computation of nonlinear deformations with high degrees of freedom. Often it takes a significant amount of computation time and thus becomes infeasible for practical purposes. In this paper, we present a solution based on two key ideas: a new registration method that generates a mapping between anatomies represented as a multicompartment model of class posterior images and geometries and an implementation of the algorithm using particle mesh approximation on Graphical Processing Units (GPUs) to fulfill the computational requirements. We show results on the registrations of neonatal to 2-year old infant MRIs. Quantitative validation demonstrates that our proposed method generates registrations that better maintain the consistency of anatomical structures over time and provides transformations that better preserve structures undergoing large deformations than transformations obtained by standard intensity-only registration. We also achieve the speedup of three orders of magnitudes compared to a CPU reference implementation, making it possible to use the technique in time-critical applications

Towards extending the SWITCH platform for time-critical, cloud-based CUDA applications: Job scheduling parameters influencing performance

SWITCH (Software Workbench for Interactive, Time Critical and Highly self-adaptive cloud applications) allows for the development and deployment of real-time applications in the cloud, but it does not yet support instances backed by Graphics Processing Units (GPUs). Wanting to explore how SWITCH might support CUDA (a GPU architecture) in the future, we have undertaken a review of time-critical CUDA applications, discovering that run-time requirements (which we call ‘wall time’) are in many cases regarded as the most important. We have performed experiments to investigate which parameters have the greatest impact on wall time when running multiple Amazon Web Services GPU-backed instances. Although a maximum of 8 single-GPU instances can be launched in a single Amazon Region, launching just 2 instances rather than 1 gives a 42% decrease in wall time. Also, instances are often wasted doing nothing, and there is a moderately-strong relationship between how problems are distributed across instances and wall time. These findings can be used to enhance the SWITCH provision for specifying Non-Functional Requirements (NFRs); in the future, GPU-backed instances could be supported. These findings can also be used more generally, to optimise the balance between the computational resources needed and the resulting wall time to obtain results