Accelerating computational diffusion MRI using Graphics Processing Units

Thesis

Diffusion magnetic resonance imaging (dMRI) allows uniquely the study of the human brain non-invasively and in vivo. Advances in dMRI offer new insight into tissue microstructure and connectivity, and the possibility of investigating the mechanisms and pathology of neurological diseases. The great potential of the technique relies on indirect inference, as modelling frameworks are necessary to map dMRI measurements to neuroanatomical features. However, this mapping can be computationally expensive, particularly given the trend of increasing dataset sizes and/or the increased complexity in biophysical modelling. Limitations on computing can restrict data exploration and even methodology development. A step forward is to take advantage of the power offered by recent parallel computing architectures, especially Graphics Processing Units (GPUs). GPUs are massive parallel processors that offer trillions of floating point operations per second, and have made possible the solution of computationally intensive scientific problems that were intractable before. However, they are not inherently suited for all types of problems, and bespoke computational frameworks need to be developed in many cases to take advantage of their full potential.

In this thesis, we propose parallel computational frameworks for the analysis of dMRI using GPUs within different contexts. We show that GPU-based designs can offer accelerations of more than two orders of magnitude for a number of scientific computing tasks with different parallelisability requirements, ranging from biophysical modelling for tissue microstructure estimation to white matter tractography for connectome generation. We develop novel and efficient GPUaccelerated solutions, including a framework that automatically generates GPU parallel code from a user-specified biophysical model. We also present a parallel GPU framework for performing probabilistic tractography and generating whole-brain connectomes. Throughout the thesis, we discuss several strategies for parallelising scientific applications, and we show the great potential of the accelerations obtained, which change the perspective of what is computationally feasible.

Authors: Hernandez-Fernandez, M

• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: Non-linear optimisation; GPGPU; Diffusion MRI; Tractography; Scientific computing; Connectome; Brain Modelling; Brain microstructure
• Subjects: Graphics processing units; Computational diffusion MRI