Functional Neuroimaging Data Characterisation Via Tensor Representations

The growing interest in neuroimaging technologies generates a massive amount of biomedical data that exhibit high dimensionality. Tensor-based analysis of brain imaging data has by now been recognized as an effective approach exploiting its inherent multi-way nature. In particular, the advantages of tensorial over matrix-based methods have previously been demonstrated in the context of functional magnetic resonance imaging (fMRI) source localization; the identification of the regions of the brain which are activated at specific time instances. However, such methods can also become ineffective in realistic challenging scenarios, involving, e.g., strong noise and/or significant overlap among the activated regions. Moreover, they commonly rely on the assumption of an underlying multilinear model generating the data. In the first part of this thesis, we aimed at investigating the possible gains from exploiting the 3-dimensional nature of the brain images, through a higher-order tensorization ...

Christos Chatzichristos — National and Kapodistrian University of Athens


Learning from structured EEG and fMRI data supporting the diagnosis of epilepsy

Epilepsy is a neurological condition that manifests in epileptic seizures as a result of an abnormal, synchronous activity of a large group of neurons. Depending on the affected brain regions, seizures produce various severe clinical symptoms. Epilepsy cannot be cured and in many cases is not controlled by medication either. Surgical resection of the region responsible for generating the epileptic seizures might offer remedy for these patients. Electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) measure the changes of brain activity in time over different locations of the brain. As such, they provide valuable information on the nature, the timing and the spatial origin of the epileptic activity. Unfortunately, both techniques record activity of different brain and artefact sources as well. Hence, EEG and fMRI signals are characterised by low signal to noise ratio. Data quality and the vast amount ...

Hunyadi, Borbála — KU Leuven


Improving data-driven EEG-FMRI analyses for the study of cognitive functioning

Understanding the cognitive processes that are going on in the human brain, requires the combination of several types of observations. For this reason, since several years, neuroscience research started to focus on multimodal approaches. One such multimodal approach is the combination of electroencephalography (EEG) and functional magnetic resonance imaging (fMRI). The non-invasive character of these two modalities makes their combination not only harmless and painless, but also especially suited for widespread research in both clinical and experimental applications. Moreover, the complementarity between the high temporal resolution of the EEG and the high spatial resolution of the fMRI, allows obtaining a more complete picture of the processes under study. However, the combination of EEG and fMRI is challenging, not only on the level of the data acquisition, but also when it comes to extracting the activity of interest and interpreting the ...

Vanderperren, Katrien — KU Leuven


Blind Source Separation of functional dynamic MRI signals via Dictionary Learning

Magnetic Resonance Imaging (MRI) constitutes a non-invasive medical imaging technique that allows the exploration of the inner anatomy, tissues, and physiological processes of the body. Among the different MRI applications, functional Magnetic Resonance Imaging (fMRI) has slowly become an essential tool for investigating the brain behavior and, nowadays, it plays a fundamental role in clinical and neurophysiological research. Due to its particular nature, specialized signal processing techniques are required in order to analyze the fMRI data properly. Among the various related techniques that have been developed over the years, the General Linear Model (GLM) is one of the most widely used approaches, and it usually appears as a default in many specialized software toolboxes for fMRI. On the other end, Blind Source Separation (BSS) methods constitute the most common alternative to GLM, especially when no prior information regarding the brain ...

Morante, Manuel — National and Kapodistrian University of Athens


Methods for functional connectivity and morphometry in neonatal neuroimaging to study neurodevelopment

Preterm birth is a major pediatric health problem that perturbs the genetically determined program of corticogenesis of the developing brain. As a consequence, prematurity has been strongly associated with adverse long-term neurodevelopmental outcome that may persist even into adulthood. Early characterization of the underlying neuronal mechanisms and early identification of infants at risk is of paramount importance since it allows better development of early therapeutic interventions aiming to prevent adverse outcomes through resilience. This dissertation aims to investigate the consequences of preterm birth on brain function and structure and their relation to adverse neurodevelopmental outcome, as well as to unveil the effect of an early music intervention on brain function. Research to date has mainly focused on the effect of early interventions on the long-term outcome but not on the effect of those interventions on brain function in preterm populations. ...

Loukas, Serafeim — Swiss Federal Institute of Technology Lausanne (EPFL)


Optimal estimation of diffusion MRI parameters

Diffusion magnetic resonance imaging (dMRI) is currently the method of choice for the in vivo and non-invasive quantification of water diffusion in biological tissue. Several diffusion models have been proposed to obtain quantitative diffusion parameters, which have shown to provide novel information on the structural and organizational features of biological tissue, the brain white matter in particular. The goal of this dissertation is to improve the accuracy of the diffusion parameter estimation, given the non-Gaussian nature of the diffusion-weighted MR data. In part I of this manuscript, the necessary basics of dMRI are provided. Next, Part II deals with diffusion parameter estimation and includes the main contributions of the research. Finally, Part III covers the construction of a population-based dMRI atlas of the rat brain.

Veraart, Jelle — University of Antwerp


Localisation of Brain Functions: Stimuling Brain Activity and Source Reconstruction for Classification

A key issue in understanding how the brain functions is the ability to correlate functional information with anatomical localisation. Functional information can be provided by a variety of techniques like positron emission tomography (PET), functional MRI (fMRI), electroencephalography (EEG), magnetoencephalography (MEG) or transcranial magnetic stimulation (TMS). All these methods provide different, but complementary, information about the functional areas of the brain. PET and fMRI provide spatially accurate picture of brain regions involved in a given task. TMS permits to infer the contribution of the stimulated brain area to the task under investigation. EEG and MEG, which reflects brain activity directly, have temporal accuracy of the order of a millisecond. TMS, EEG and MEG are offset by their low spatial resolution. In this thesis, we propose two methods to improve the spatial accuracy of method based on TMS and EEG. The ...

Noirhomme, Quentin — Katholieke Universiteit Leuven


Central and peripheral mechanisms: a multimodal approach to understanding and restoring human motor control

All human actions involve motor control. Even the simplest movement requires the coordinated recruitment of many muscles, orchestrated by neuronal circuits in the brain and the spinal cord. As a consequence, lesions affecting the central nervous system, such as stroke, can lead to a wide range of motor impairments. While a certain degree of recovery can often be achieved by harnessing the plasticity of the motor hierarchy, patients typically struggle to regain full motor control. In this context, technology-assisted interventions offer the prospect of intense, controllable and quantifiable motor training. Yet, clinical outcomes remain comparable to conventional approaches, suggesting the need for a paradigm shift towards customized knowledge-driven treatments to fully exploit their potential. In this thesis, we argue that a detailed understanding of healthy and impaired motor pathways can foster the development of therapies optimally engaging plasticity. To this ...

Kinany, Nawal — Ecole Polytechnique Fédérale de Lausanne (EPFL)


Dynamics of Brain Function in Preterm-Born Young Adolescents

Preterm birth is a major risk factor for neurodevelopment impairments often only appearing later in life. The brain is still at a high rate of development during adolescence, making this a promising window for intervention. It is thus crucial to understand the mechanisms of altered brain function in this population. The aim of this thesis is to investigate how the brain dynamically reconfigures its own organisation over time in preterm-born young adolescents. Research to date has mainly focused on structural disturbances or in static features of brain function in this population. However, recent studies have shown that brain activity is highly dynamic, both spontaneously and during performance of a task, and that small disruptions in its complex architecture may interfere with normal behaviour and cognitive abilities. This thesis explores the dynamic nature of brain function in preterm-born adolescents in three ...

Freitas, Lorena G. A. — École Polytechnique Fédérale de Lausanne


Data-Driven Multimodal Signal Processing With Applications To EEG-fMRI Fusion

Most cognitive processes in the brain are reflected through several aspects simultaneously, allowing us to observe the same process from different biological phenomena. The diverse nature of these biological processes suggests that a better understanding of cerebral activity may be achieved through multimodal measurements. One of the possible multimodal brain recording settings is the combination of electroencephalography (EEG) and functional magnetic resonance imaging (fMRI), which is one of the main topics of this thesis. Two groups of EEG-fMRI integration approaches are possible. The first group, commonly called model-based techniques, are very popular due to the fact that the results from such analyses confirm or disprove a specific hypothesis. However, such hypotheses are not always available, requiring a more explorative approach to analyze the data. This exploration is possible with the second group of approaches, the so-called data-driven methods. The data-driven ...

Mijović, Bogdan — KU Leuven


Advances in graph signal processing: Graph filtering and network identification

To the surprise of most of us, complexity in nature spawns from simplicity. No matter how simple a basic unit is, when many of them work together, the interactions among these units lead to complexity. This complexity is present in the spreading of diseases, where slightly different policies, or conditions,might lead to very different results; or in biological systems where the interactions between elements maintain the delicate balance that keep life running. Fortunately, despite their complexity, current advances in technology have allowed us to have more than just a sneak-peak at these systems. With new views on how to observe such systems and gather data, we aimto understand the complexity within. One of these new views comes from the field of graph signal processing which provides models and tools to understand and process data coming from such complex systems. With ...

Coutino, Mario — Delft University of Technology


Dynamic organization of human brain function and its relevance for psychosis vulnerability

The brain is the substrate of a complex dynamic system providing a remarkably varied range of functionalities, going from simple perception to higher-level cognition. Disturbances in its complex dynamics can cause an equally vast variety of mental disorders. One such brain disorder is schizophrenia, a neurodevelopmental disease characterized by abnormal perception of reality that manifests in symptoms like hallucinations or delusions. Even though the brain is known to be affected in schizophrenia, the exact pathophysiology underlying its developmental course is still mostly unknown. In this thesis, we develop and apply methods to look into ongoing brain function measured through magnetic resonance imaging (MRI) and evaluate the potential of these approaches for improving our understanding of psychosis vulnerability and schizophrenia. We focus on patients with chromosome 22q11.2 deletion syndrome (22q11DS), a genetic disorder that comes with a 30fold increased risk for ...

Zöller, Daniela — EPFL (École Polytechnique Fédérale de Lausanne)


Segmentation par modèle déformable surfacique localement régularisé par spline

Image segmentation through deformable models is a method that localizes object boundaries. When difficult segmentation context are proposed because of noise or a lack of information, the use of prior knowledge in the deformation process increases segmentation accuracy. Medical imaging is often concerned by these context. Moreover, medical applications deal with large amounts of data. Then it is mandatory to use a robust and fast processing. This question lead us to a local regularisation of the deformable model. Highly based on the active contour framework, also known as \emph{snake}, we propose a new regularization scheme. This is done by filtering the displacements at each iteration. The filter is based on a smoothing spline kernel whose aim was to approximate a set of points rather than interpolating it. We point out the consistency of the regularization parameter in such a method. ...

Velut, Jerome — INSA-Lyon / CREATIS-LRMN


Non-Intrusive Speech Intelligibility Prediction

The ability to communicate through speech is important for social interaction. We rely on the ability to communicate with each other even in noisy conditions. Ideally, the speech is easy to understand but this is not always the case, if the speech is degraded, e.g., due to background noise, distortion or hearing impairment. One of the most important factors to consider in relation to such degradations is speech intelligibility, which is a measure of how easy or difficult it is to understand the speech. In this thesis, the focus is on the topic of speech intelligibility prediction. The thesis consists of an introduction to the field of speech intelligibility prediction and a collection of scientific papers. The introduction provides a background to the challenges with speech communication in noisy conditions, followed by an introduction to how speech is produced and ...

Sørensen, Charlotte — Aalborg University


Transformation methods in signal processing

This dissertation is concerned with the application of the theory of rational functions in signal processing. The PhD thesis summarizes the corresponding results of the author’s research. Since the systems of rational functions are defined by the collection of inverse poles with multiplicities, the following parameters should be determined: the number, the positions and the multiplicities of the inverse poles. Therefore, we develop the hyperbolic variant of the so-called Nelder–Mead and the particle swarm optimization algorithm. In addition, the latter one is integrated into a more general multi-dimensional framework. Furthermore, we perform a detailed stability and error analysis of these methods. We propose an electrocardiogram signal generator based on spline interpolation. It turns to be an efficient tool for testing and evaluating signal models, filtering techniques, etc. In this thesis, the synthesized heartbeats are used to test the diagnostic distortion ...

Kovács, Péter — Eötvös L. University, Budapest, Hungary

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