Signal processing in diffusion MRI : high quality signal reconstruction

Magnetic Resonance Imaging (MRI) is a medical imaging technique which is especially sensitive to different soft tissues, producing a good contrast between them. It allows for in vivo visualisation of internal structures in detail and became an indispensable tool in diagnosing and monitoring the brain related diseases and pathologies. Amongst others, MRI can be used to measure random incoherent motion of water molecules, which in turn allows to infer structural information. One of the main challenges in processing and analysing four dimensional diffusion MRI images is low signal quality. To improve the signal quality, either denoising algorithm or angular and spatial regularisations are utilised. Regularisation method based on Laplace--Beltrami smoothing operator was successfully applied to diffusion signal. In this thesis, a new regularisation strength selection scheme for diffusion signal regularisation is introduced. A mathematical model of diffusion signal is used in Monte--Carlo simulations, and a regularisation strength that optimally reconstructs the diffusion signal is sought. The regularisation values found in this research show a different trend than the currently used L-curve analysis, and further improve reconstruction accuracy. Additionally, as an alternative to regularisation methods a backward elimination regression for spherical harmonics is proposed. Instead of using the regularisation term as a low-pass filter, the statistical t-test is classifying regression terms into reliable and corrupted. Four algorithms that use this information are further introduced. As the result, a selective filtering is constructed that retains the angular sharpness of the signal, while at the same time reducing corruptive effect of measurement noise. Finally, a statistical approach for estimating diffusion signal is investigated. Based on the physical properties of water diffusion a prior knowledge for the diffusion signal is constructed. The spherical harmonic transform is then formulated as a Bayesian regression problem. Diffusion signal reconstructed with the addition of such prior knowledge is accurate, noise resilient, and of high quality

Signal processing in diffusion MRI : high quality signal reconstruction

Magnetic Resonance Imaging (MRI) is a medical imaging technique which is especially sensitive to different soft tissues, producing a good contrast between them. It allows for in vivo visualisation of internal structures in detail and became an indispensable tool in diagnosing and monitoring the brain related diseases and pathologies. Amongst others, MRI can be used to measure random incoherent motion of water molecules, which in turn allows to infer structural information. One of the main challenges in processing and analysing four dimensional diffusion MRI images is low signal quality. To improve the signal quality, either denoising algorithm or angular and spatial regularisations are utilised. Regularisation method based on Laplace--Beltrami smoothing operator was successfully applied to diffusion signal. In this thesis, a new regularisation strength selection scheme for diffusion signal regularisation is introduced. A mathematical model of diffusion signal is used in Monte--Carlo simulations, and a regularisation strength that optimally reconstructs the diffusion signal is sought. The regularisation values found in this research show a different trend than the currently used L-curve analysis, and further improve reconstruction accuracy. Additionally, as an alternative to regularisation methods a backward elimination regression for spherical harmonics is proposed. Instead of using the regularisation term as a low-pass filter, the statistical t-test is classifying regression terms into reliable and corrupted. Four algorithms that use this information are further introduced. As the result, a selective filtering is constructed that retains the angular sharpness of the signal, while at the same time reducing corruptive effect of measurement noise. Finally, a statistical approach for estimating diffusion signal is investigated. Based on the physical properties of water diffusion a prior knowledge for the diffusion signal is constructed. The spherical harmonic transform is then formulated as a Bayesian regression problem. Diffusion signal reconstructed with the addition of such prior knowledge is accurate, noise resilient, and of high quality

Spherical harmonics for surface parametrisation and remeshing

This paper proposes a novel method for parametrisation and remeshing incomplete and irregular polygonal meshes. Spherical harmonics basis functions are used for parametrisation. This involves least squares fitting of spherical harmonics basis functions to the surface mesh. Tikhonov regularisation is then used to improve the parametrisation before remeshing the surface. Experiments show that the proposed techniques are effective for parametrising and remeshing polygonal meshes

Determination of superoxide in seawater using 2-methyl-6-(4-methoxyphenyl)-3,7- dihydroimidazo[1,2-a]pyrazin-3(7H)-one chemiluminescence

Superoxide, the one-electron reduced form of dioxygen, is known to be generated in marine environments by photochemical and biological processes. Because of its selective reaction with only a few commonly occurring compounds, superoxide is expected to approach concentrations in the high picomolar or low nanomolar range in seawater. Most currently existing methods do not have both the necessary sensitivity and selectivity to measure naturally occurring concentrations. In contrast, we demonstrate here that the chemiluminescence reagent 2-methyl-6-(4-methoxyphenyl)-3,7-dihydroimidazo[l,2-a]pyrazin-3(7H)-one (MCLA) is selective for superoxide in seawater and can be used with a detection limit of around 50 pM. Although a wide range of potential interferences were shown not to react with MCLA directly, some care must be taken when analyzing samples containing nanomolar concentrations of Fe(II), Cu(I), Mo(V), V(III), or V(IV), since these compounds can react with oxygen to produce superoxide during analysis that is subsequently detected. We describe two methods for calibrating the system, one employing photochemically generated superoxide standards and the other employing the superoxide-generating xanthine/xanthine oxidase system and discuss limitations on the use of each. The method was successfully used in the field to determine steady-state superoxide concentrations in the water column in the eastern equatorial Pacific Ocean