(k,q)-Compressed Sensing for dMRI with Joint Spatial-Angular Sparsity Prior

Advanced diffusion magnetic resonance imaging (dMRI) techniques, like diffusion spectrum imaging (DSI) and high angular resolution diffusion imaging (HARDI), remain underutilized compared to diffusion tensor imaging because the scan times needed to produce accurate estimations of fiber orientation are significantly longer. To accelerate DSI and HARDI, recent methods from compressed sensing (CS) exploit a sparse underlying representation of the data in the spatial and angular domains to undersample in the respective k- and q-spaces. State-of-the-art frameworks, however, impose sparsity in the spatial and angular domains separately and involve the sum of the corresponding sparse regularizers. In contrast, we propose a unified (k,q)-CS formulation which imposes sparsity jointly in the spatial-angular domain to further increase sparsity of dMRI signals and reduce the required subsampling rate. To efficiently solve this large-scale global reconstruction problem, we introduce a novel adaptation of the FISTA algorithm that exploits dictionary separability. We show on phantom and real HARDI data that our approach achieves significantly more accurate signal reconstructions than the state of the art while sampling only 2-4% of the (k,q)-space, allowing for the potential of new levels of dMRI acceleration.Comment: To be published in the 2017 Computational Diffusion MRI Workshop of MICCA

Sparse image reconstruction on the sphere: implications of a new sampling theorem

We study the impact of sampling theorems on the fidelity of sparse image reconstruction on the sphere. We discuss how a reduction in the number of samples required to represent all information content of a band-limited signal acts to improve the fidelity of sparse image reconstruction, through both the dimensionality and sparsity of signals. To demonstrate this result we consider a simple inpainting problem on the sphere and consider images sparse in the magnitude of their gradient. We develop a framework for total variation (TV) inpainting on the sphere, including fast methods to render the inpainting problem computationally feasible at high-resolution. Recently a new sampling theorem on the sphere was developed, reducing the required number of samples by a factor of two for equiangular sampling schemes. Through numerical simulations we verify the enhanced fidelity of sparse image reconstruction due to the more efficient sampling of the sphere provided by the new sampling theorem.Comment: 11 pages, 5 figure

An Optimal Dimensionality Sampling Scheme on the Sphere for Antipodal Signals In Diffusion Magnetic Resonance Imaging

We propose a sampling scheme on the sphere and develop a corresponding spherical harmonic transform (SHT) for the accurate reconstruction of the diffusion signal in diffusion magnetic resonance imaging (dMRI). By exploiting the antipodal symmetry, we design a sampling scheme that requires the optimal number of samples on the sphere, equal to the degrees of freedom required to represent the antipodally symmetric band-limited diffusion signal in the spectral (spherical harmonic) domain. Compared with existing sampling schemes on the sphere that allow for the accurate reconstruction of the diffusion signal, the proposed sampling scheme reduces the number of samples required by a factor of two or more. We analyse the numerical accuracy of the proposed SHT and show through experiments that the proposed sampling allows for the accurate and rotationally invariant computation of the SHT to near machine precision accuracy.Comment: Will be published in the proceedings of the International Conference Acoustics, Speech and Signal Processing 2015 (ICASSP'2015

Optimal-Dimensionality Sampling on the Sphere: Improvements and Variations

For the accurate representation and reconstruction of band-limited signals on the sphere, an optimal-dimensionality sampling scheme has been recently proposed which requires the optimal number of samples equal to the number of degrees of freedom of the signal in the spectral (harmonic) domain. The computation of the spherical harmonic transform (SHT) associated with the optimal-dimensionality sampling requires the inversion of a series of linear systems in an iterative manner. The stability of the inversion depends on the placement of iso-latitude rings of samples along co-latitude. In this work, we have developed a method to place these iso-latitude rings of samples with the objective of improving the well-conditioning of the linear systems involved in the computation of the SHT. We also propose a multi-pass SHT algorithm to iteratively improve the accuracy of the SHT of band-limited signals. Furthermore, we review the changes in the computational complexity and improvement in accuracy of the SHT with the embedding of the proposed methods. Through numerical experiments, we illustrate that the proposed variations and improvements in the SHT algorithm corresponding to the optimal-dimensionality sampling scheme significantly enhance the accuracy of the SHT.Comment: 5 Pages, 4 figure

Sampling Sparse Signals on the Sphere: Algorithms and Applications

We propose a sampling scheme that can perfectly reconstruct a collection of spikes on the sphere from samples of their lowpass-filtered observations. Central to our algorithm is a generalization of the annihilating filter method, a tool widely used in array signal processing and finite-rate-of-innovation (FRI) sampling. The proposed algorithm can reconstruct $K$ spikes from $(K+\sqrt{K})^2$ spatial samples. This sampling requirement improves over previously known FRI sampling schemes on the sphere by a factor of four for large $K$. We showcase the versatility of the proposed algorithm by applying it to three different problems: 1) sampling diffusion processes induced by localized sources on the sphere, 2) shot noise removal, and 3) sound source localization (SSL) by a spherical microphone array. In particular, we show how SSL can be reformulated as a spherical sparse sampling problem.Comment: 14 pages, 8 figures, submitted to IEEE Transactions on Signal Processin

Spherical deconvolution of multichannel diffusion MRI data with non-Gaussian noise models and spatial regularization

Spherical deconvolution (SD) methods are widely used to estimate the intra-voxel white-matter fiber orientations from diffusion MRI data. However, while some of these methods assume a zero-mean Gaussian distribution for the underlying noise, its real distribution is known to be non-Gaussian and to depend on the methodology used to combine multichannel signals. Indeed, the two prevailing methods for multichannel signal combination lead to Rician and noncentral Chi noise distributions. Here we develop a Robust and Unbiased Model-BAsed Spherical Deconvolution (RUMBA-SD) technique, intended to deal with realistic MRI noise, based on a Richardson-Lucy (RL) algorithm adapted to Rician and noncentral Chi likelihood models. To quantify the benefits of using proper noise models, RUMBA-SD was compared with dRL-SD, a well-established method based on the RL algorithm for Gaussian noise. Another aim of the study was to quantify the impact of including a total variation (TV) spatial regularization term in the estimation framework. To do this, we developed TV spatially-regularized versions of both RUMBA-SD and dRL-SD algorithms. The evaluation was performed by comparing various quality metrics on 132 three-dimensional synthetic phantoms involving different inter-fiber angles and volume fractions, which were contaminated with noise mimicking patterns generated by data processing in multichannel scanners. The results demonstrate that the inclusion of proper likelihood models leads to an increased ability to resolve fiber crossings with smaller inter-fiber angles and to better detect non-dominant fibers. The inclusion of TV regularization dramatically improved the resolution power of both techniques. The above findings were also verified in brain data

Unified Heat Kernel Regression for Diffusion, Kernel Smoothing and Wavelets on Manifolds and Its Application to Mandible Growth Modeling in CT Images

We present a novel kernel regression framework for smoothing scalar surface data using the Laplace-Beltrami eigenfunctions. Starting with the heat kernel constructed from the eigenfunctions, we formulate a new bivariate kernel regression framework as a weighted eigenfunction expansion with the heat kernel as the weights. The new kernel regression is mathematically equivalent to isotropic heat diffusion, kernel smoothing and recently popular diffusion wavelets. Unlike many previous partial differential equation based approaches involving diffusion, our approach represents the solution of diffusion analytically, reducing numerical inaccuracy and slow convergence. The numerical implementation is validated on a unit sphere using spherical harmonics. As an illustration, we have applied the method in characterizing the localized growth pattern of mandible surfaces obtained in CT images from subjects between ages 0 and 20 years by regressing the length of displacement vectors with respect to the template surface.Comment: Accepted in Medical Image Analysi