Spatiotemporal techniques in multimodal imaging for brain mapping and epilepsy

Thesis (Ph.D.)--Boston UniversityThis thesis explored multimodal brain imaging using advanced spatiotemporal techniques. The first set of experiments were based on simulations. Much controversy exists in the literature regarding the differences between magnetoencephalography (MEG) and electroencephalography (EEG}, both practically and theoretically. The differences were explored using simulations that evaluated the expected signal-to-noise ratios from reasonable brain sources. MEG and EEG were found to be complementary, with each modality optimally suited to image activity from different areas of the cortical surface. Consequently, evaluations of epileptic patients and general neuroscience experiments will both benefit from simultaneously collected MEG/EEG. The second set of experiments represent an example of MEG combined with magnetic resonance imaging (MRI) and functional MRI (fMRI) applied to healthy subjects. The study set out to resolve two questions relating to shape perception. First, does the brain activate functional areas sequentially during shape perception, as has been suggested in recent literature? Second, which , if any, functional areas are active time-locked with reaction-time? The study found that functional areas are non-sequentially activated, and that area IT is active time-locked with reaction-time. These two points, coupled with the method for multimodal integration , can help further develop our understanding of shape perception in particular, and cortical dynamics in general for healthy subjects. Broadly, these two studies represent practical guidelines for epilepsy evaluations and brain mapping studies. For epilepsy studies, clinicians could combine MEG and EEG to maximize the probability of finding the source of seizures. For brain mapping in general, EEG, MEG, MRI and fMRI can be combined in the methods outlined here to obtain more sophisticated views of cortical dynamics

Graph Theory and Networks in Biology

In this paper, we present a survey of the use of graph theoretical techniques in Biology. In particular, we discuss recent work on identifying and modelling the structure of bio-molecular networks, as well as the application of centrality measures to interaction networks and research on the hierarchical structure of such networks and network motifs. Work on the link between structural network properties and dynamics is also described, with emphasis on synchronization and disease propagation.Comment: 52 pages, 5 figures, Survey Pape

Statistical single channel source separation

PhD ThesisSingle channel source separation (SCSS) principally is one of the challenging fields in signal processing and has various significant applications. Unlike conventional SCSS methods which were based on linear instantaneous model, this research sets out to investigate the separation of single channel in two types of mixture which is nonlinear instantaneous mixture and linear convolutive mixture. For the nonlinear SCSS in instantaneous mixture, this research proposes a novel solution based on a two-stage process that consists of a Gaussianization transform which efficiently compensates for the nonlinear distortion follow by a maximum likelihood estimator to perform source separation. For linear SCSS in convolutive mixture, this research proposes new methods based on nonnegative matrix factorization which decomposes a mixture into two-dimensional convolution factor matrices that represent the spectral basis and temporal code. The proposed factorization considers the convolutive mixing in the decomposition by introducing frequency constrained parameters in the model. The method aims to separate the mixture into its constituent spectral-temporal source components while alleviating the effect of convolutive mixing. In addition, family of Itakura-Saito divergence has been developed as a cost function which brings the beneficial property of scale-invariant. Two new statistical techniques are proposed, namely, Expectation-Maximisation (EM) based algorithm framework which maximizes the log-likelihood of a mixed signals, and the maximum a posteriori approach which maximises the joint probability of a mixed signal using multiplicative update rules. To further improve this research work, a novel method that incorporates adaptive sparseness into the solution has been proposed to resolve the ambiguity and hence, improve the algorithm performance. The theoretical foundation of the proposed solutions has been rigorously developed and discussed in details. Results have concretely shown the effectiveness of all the proposed algorithms presented in this thesis in separating the mixed signals in single channel and have outperformed others available methods.Universiti Teknikal Malaysia Melaka(UTeM), Ministry of Higher Education of Malaysi

Non-uniform resolution and partial volume recovery in tomographic image reconstruction methods

Acquired data in tomographic imaging systems are subject to physical or detector based image degrading effects. These effects need to be considered and modeled in order to optimize resolution recovery. However, accurate modeling of the physics of data and acquisition processes still lead to an ill-posed reconstruction problem, because real data is incomplete and noisy. Real images are always a compromise between resolution and noise; therefore, noise processes also need to be fully considered for optimum bias variance trade off. Image degrading effects and noise are generally modeled in the reconstruction methods, while, statistical iterative methods can better model these effects, with noise processes, as compared to the analytical methods. Regularization is used to condition the problem and explicit regularization methods are considered better to model various noise processes with an extended control over the reconstructed image quality. Emission physics through object distribution properties are modeled in form of a prior function. Smoothing and edge-preserving priors have been investigated in detail and it has been shown that smoothing priors over-smooth images in high count areas and result in spatially non-uniform and nonlinear resolution response. Uniform resolution response is desirable for image comparison and other image processing tasks, such as segmentation and registration. This work proposes methods, based on MRPs in MAP estimators, to obtain images with almost uniform and linear resolution characteristics, using nonlinearity of MRPs as a correction tool. Results indicate that MRPs perform better in terms of response linearity, spatial uniformity and parameter sensitivity, as compared to QPs and TV priors. Hybrid priors, comprised of MRPs and QPs, have been developed and analyzed for their activity recovery performance in two popular PVC methods and for an analysis of list-mode data reconstruction methods showing that MPRs perform better than QPs in different situations

Magnetoencephalography

This is a practical book on MEG that covers a wide range of topics. The book begins with a series of reviews on the use of MEG for clinical applications, the study of cognitive functions in various diseases, and one chapter focusing specifically on studies of memory with MEG. There are sections with chapters that describe source localization issues, the use of beamformers and dipole source methods, as well as phase-based analyses, and a step-by-step guide to using dipoles for epilepsy spike analyses. The book ends with a section describing new innovations in MEG systems, namely an on-line real-time MEG data acquisition system, novel applications for MEG research, and a proposal for a helium re-circulation system. With such breadth of topics, there will be a chapter that is of interest to every MEG researcher or clinician

Brain connectivity analysis from EEG signals using stable phase-synchronized states during face perception tasks

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this recordDegree of phase synchronization between different Electroencephalogram (EEG) channels is known to be the manifestation of the underlying mechanism of information coupling between different brain regions. In this paper, we apply a continuous wavelet transform (CWT) based analysis technique on EEG data, captured during face perception tasks, to explore the temporal evolution of phase synchronization, from the onset of a stimulus. Our explorations show that there exists a small set (typically 3-5) of unique synchronized patterns or synchrostates, each of which are stable of the order of milliseconds. Particularly, in the beta (β) band, which has been reported to be associated with visual processing task, the number of such stable states has been found to be three consistently. During processing of the stimulus, the switching between these states occurs abruptly but the switching characteristic follows a well-behaved and repeatable sequence. This is observed in a single subject analysis as well as a multiple-subject group-analysis in adults during face perception. We also show that although these patterns remain topographically similar for the general category of face perception task, the sequence of their occurrence and their temporal stability varies markedly between different face perception scenarios (stimuli) indicating toward different dynamical characteristics for information processing, which is stimulus-specific in nature. Subsequently, we translated these stable states into brain complex networks and derived informative network measures for characterizing the degree of segregated processing and information integration in those synchrostates, leading to a new methodology for characterizing information processing in human brain. The proposed methodology of modeling the functional brain connectivity through the synchrostates may be viewed as a new way of quantitative characterization of the cognitive ability of the subject, stimuli and information integration/segregation capability.The work presented in this paper was supported by FP7 EU funded MICHELANGELO project, Grant Agreement #288241. Website: www.michelangelo-project.eu/

Interdisciplinary application of nonlinear time series methods

This paper reports on the application to field measurements of time series methods developed on the basis of the theory of deterministic chaos. The major difficulties are pointed out that arise when the data cannot be assumed to be purely deterministic and the potential that remains in this situation is discussed. For signals with weakly nonlinear structure, the presence of nonlinearity in a general sense has to be inferred statistically. The paper reviews the relevant methods and discusses the implications for deterministic modeling. Most field measurements yield nonstationary time series, which poses a severe problem for their analysis. Recent progress in the detection and understanding of nonstationarity is reported. If a clear signature of approximate determinism is found, the notions of phase space, attractors, invariant manifolds etc. provide a convenient framework for time series analysis. Although the results have to be interpreted with great care, superior performance can be achieved for typical signal processing tasks. In particular, prediction and filtering of signals are discussed, as well as the classification of system states by means of time series recordings.Comment: 86 pages, 26 figure

Statistical Analysis of EEG Phase Shift Events

This thesis develops statistical methods for the identification, and analysis of phase shift events, i.e. sudden changes in the timing relationship between coupled oscillators. Phase shifts events occur in many complex systems but here the primary interest is the analysis of electroencephalogram (EEG) recordings where they have been identified as markers of information transmission in the brain; as a secondary example we analyze systems of weakly coupled Rossler attractors. The main result, found in Chapter 2, is a novel method for estimating neural connectivity from EEG recordings based on spatio-temporal patterns of phase shift events. Phase shift events are modelled as a multivariate point process, and the ideas of Granger causality are used to motivate a directed measure of connectivity. The method is demonstrated on EEG recordings from 18 participants during three task conditions; resting, visual vigilance and auditory vigilance. Likelihood ratios are used to test the hypothesis of no Granger causal interaction between signals, and network patterns are analyzed using graph theory. In Chapter 3 the problem of phase shift identification is formulated as a change point in the instantaneous phase. Two estimators are considered, based on the cumulative summation and the instantaneous phase derivative. Block bootstrapping techniques are used to capture the dependency structure in the signals and determine critical values for shift identification. Estimators are evaluated both on their accuracy, and temporal resolution. Finally, detailed simulation studies are performed using realistic head models to investigate the effect of volume conduction (linear spread of electrical activity at the scalp) on phase shift analysis. Specifically, Chapter 4 investigates the effect of volume conduction on the analysis, in order to understand the limitations of the phase shift Granger causality method. Chapter 5 then investigates an approach for reducing the effect of volume conduction by using EEG source reconstruction techniques to estimate neural source activity and then identifying phase shifts with-in the brain directly from the reconstructed sources. The primary impact is the novel method for estimating neural connectivity. Each chapter investigates a different aspect of EEG phase analysis, and together they form a complete package for estimation and interpretation of neural connectivity. Two other areas of impact are in statistical change point analysis, and behavioural psychology

Frequency domain high density diffuse optical tomography for functional brain imaging

Measurements of dynamic near-infrared (NIR) light attenuation across the human head together with model-based image reconstruction algorithms allow the recovery of three-dimensional spatial brain activation maps. Previous studies using high-density diffuse optical tomography (HD-DOT) systems have reported improved image quality over sparse arrays. Modulated NIR light, known as Frequency Domain (FD) NIR, enables measurements of phase shift along with amplitude attenuation. It is hypothesised that the utilization of these two sets of complementary data (phase and amplitude) for brain activity detection will result in an improvement in reconstructed image quality within HD-DOT. However, parameter recovery in DOT is a computationally expensive algorithm, especially when FD-HD measurements are required over a large and complex volume, as in the case of brain functional imaging. Therefore, computational tools for the light propagation modelling, known as the forward model, and the parameter recovery, known as the inverse problem, have been developed, in order to enable FD-HD-DOT. The forward model, within a diffusion approximation-based finite-element modelling framework, is accelerated by employing parallelization. A 10-fold speed increase when GPU architectures are available is achieved while maintaining high accuracy. For a very high-resolution finite-element model of the adult human head with ∼600,000 nodes, light propagation can be calculated at ∼0.25s per excitation source. Additionally, a framework for the sparse formulation of the inverse model, incorporating parallel computing, is proposed, achieving a 10-fold speed increase and a 100-fold memory efficiency, whilst maintaining reconstruction quality. Finally, to evaluate image reconstruction with and without the additional phase information, point spread functions have been simulated across a whole-scalp field of view in 24 subject-specific anatomical models using an experimentally derived noise model. The addition of phase information has shown to improve the image quality by reducing localization error by up to 59%, effective resolution by up to 21%, and depth penetration up to 5mm, as compared to using the intensity attenuation measurements alone. In addition, experimental data collected during a retinotopic experiment reveal that the phase data contains unique information about brain activity and enables images to be resolved for deeper brain regions