High resolution in-vivo MR-STAT using a matrix-free and parallelized reconstruction algorithm

MR-STAT is a recently proposed framework that allows the reconstruction of multiple quantitative parameter maps from a single short scan by performing spatial localisation and parameter estimation on the time domain data simultaneously, without relying on the FFT. To do this at high-resolution, specialized algorithms are required to solve the underlying large-scale non-linear optimisation problem. We propose a matrix-free and parallelized inexact Gauss-Newton based reconstruction algorithm for this purpose. The proposed algorithm is implemented on a high performance computing cluster and is demonstrated to be able to generate high-resolution ($1mm \times 1mm$ in-plane resolution) quantitative parameter maps in simulation, phantom and in-vivo brain experiments. Reconstructed $T_1$ and $T_2$ values for the gel phantoms are in agreement with results from gold standard measurements and for the in-vivo experiments the quantitative values show good agreement with literature values. In all experiments short pulse sequences with robust Cartesian sampling are used for which conventional MR Fingerprinting reconstructions are shown to fail.Comment: Accepted by NMR in Biomedicine on 2019-12-0

Quantitative photoacoustic tomography with piecewise constant material parameters

The goal of quantitative photoacoustic tomography is to determine optical and acoustical material properties from initial pressure maps as obtained, for instance, from photoacoustic imaging. The most relevant parameters are absorption, diffusion and Grueneisen coefficients, all of which can be heterogeneous. Recent work by Bal and Ren shows that in general, unique reconstruction of all three parameters is impossible, even if multiple measurements of the initial pressure (corresponding to different laser excitation directions at a single wavelength) are available. Here, we propose a restriction to piecewise constant material parameters. We show that in the diffusion approximation of light transfer, piecewise constant absorption, diffusion and Gr\"uneisen coefficients can be recovered uniquely from photoacoustic measurements at a single wavelength. In addition, we implemented our ideas numerically and tested them on simulated three-dimensional data

A variational method for quantitative photoacoustic tomography with piecewise constant coefficients

In this article, we consider the inverse problem of determining spatially heterogeneous absorption and diffusion coefficients from a single measurement of the absorbed energy (in the steady-state diffusion approximation of light transfer). This problem, which is central in quantitative photoacoustic tomography, is in general ill-posed since it admits an infinite number of solution pairs. We show that when the coefficients are known to be piecewise constant functions, a unique solution can be obtained. For the numerical determination of the coefficients, we suggest a variational method based based on an Ambrosio-Tortorelli-approximation of a Mumford-Shah-like functional, which we implemented numerically and tested on simulated two-dimensional data

A Novel Self-Intersection Penalty Term for Statistical Body Shape Models and Its Applications in 3D Pose Estimation

Statistical body shape models are widely used in 3D pose estimation due to their low-dimensional parameters representation. However, it is difficult to avoid self-intersection between body parts accurately. Motivated by this fact, we proposed a novel self-intersection penalty term for statistical body shape models applied in 3D pose estimation. To avoid the trouble of computing self-intersection for complex surfaces like the body meshes, the gradient of our proposed self-intersection penalty term is manually derived from the perspective of geometry. First, the self-intersection penalty term is defined as the volume of the self-intersection region. To calculate the partial derivatives with respect to the coordinates of the vertices, we employed detection rays to divide vertices of statistical body shape models into different groups depending on whether the vertex is in the region of self-intersection. Second, the partial derivatives could be easily derived by the normal vectors of neighboring triangles of the vertices. Finally, this penalty term could be applied in gradient-based optimization algorithms to remove the self-intersection of triangular meshes without using any approximation. Qualitative and quantitative evaluations were conducted to demonstrate the effectiveness and generality of our proposed method compared with previous approaches. The experimental results show that our proposed penalty term can avoid self-intersection to exclude unreasonable predictions and improves the accuracy of 3D pose estimation indirectly. Further more, the proposed method could be employed universally in triangular mesh based 3D reconstruction

Gradient-based quantitative image reconstruction in ultrasound-modulated optical tomography: first harmonic measurement type in a linearised diffusion formulation

Ultrasound-modulated optical tomography is an emerging biomedical imaging modality which uses the spatially localised acoustically-driven modulation of coherent light as a probe of the structure and optical properties of biological tissues. In this work we begin by providing an overview of forward modelling methods, before deriving a linearised diffusion-style model which calculates the first-harmonic modulated flux measured on the boundary of a given domain. We derive and examine the correlation measurement density functions of the model which describe the sensitivity of the modality to perturbations in the optical parameters of interest. Finally, we employ said functions in the development of an adjoint-assisted gradient based image reconstruction method, which ameliorates the computational burden and memory requirements of a traditional Newton-based optimisation approach. We validate our work by performing reconstructions of optical absorption and scattering in two- and three-dimensions using simulated measurements with 1% proportional Gaussian noise, and demonstrate the successful recovery of the parameters to within +/-5% of their true values when the resolution of the ultrasound raster probing the domain is sufficient to delineate perturbing inclusions.Comment: 12 pages, 6 figure

Accuracy of spike-train Fourier reconstruction for colliding nodes

We consider Fourier reconstruction problem for signals F, which are linear combinations of shifted delta-functions. We assume the Fourier transform of F to be known on the frequency interval [-N,N], with an absolute error not exceeding e > 0. We give an absolute lower bound (which is valid with any reconstruction method) for the "worst case" reconstruction error of F in situations where the nodes (i.e. the positions of the shifted delta-functions in F) are known to form an l elements cluster of a size h << 1. Using "decimation" reconstruction algorithm we provide an upper bound for the reconstruction error, essentially of the same form as the lower one. Roughly, our main result states that for N*h of order of (2l-1)-st root of e the worst case reconstruction error of the cluster nodes is of the same order as h, and hence the inside configuration of the cluster nodes (in the worst case scenario) cannot be reconstructed at all. On the other hand, decimation algorithm reconstructs F with the accuracy of order of 2l-st root of e