Unsupervised and semi-supervised Non-negative Matrix Factorization methods for brain tumor segmentation using multi-parametric MRI data

Gliomas represent about 80% of all malignant primary brain tumors. Despite recent advancements in glioma research, patient outcome remains poor. The 5 year survival rate of the most common and most malignant subtype, i.e. glioblastoma, is about 5%. Magnetic resonance imaging (MRI) has become the imaging modality of choice in the management of brain tumor patients. Conventional MRI (cMRI) provides excellent soft tissue contrast without exposing the patient to potentially harmful ionizing radiation. Over the past decade, advanced MRI modalities, such as perfusion-weighted imaging (PWI), diffusion-weighted imaging (DWI) and magnetic resonance spectroscopic imaging (MRSI) have gained interest in the clinical field, and their added value regarding brain tumor diagnosis, treatment planning and follow-up has been recognized. Tumor segmentation involves the imaging-based delineation of a tumor and its subcompartments. In gliomas, segmentation plays an important role in treatment planning as well ...

Sauwen, Nicolas — KU Leuven


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


Subspace-based quantification of magnetic resonance spectroscopy data using biochemical prior knowledge

Nowadays, Nuclear Magnetic Resonance (NMR) is widely used in oncology as a non-invasive diagnostic tool in order to detect the presence of tumor regions in the human body. An application of NMR is Magnetic Resonance Imaging, which is applied in routine clinical practice to localize tumors and determine their size. Magnetic Resonance Imaging is able to provide an initial diagnosis, but its ability to delineate anatomical and pathological information is significantly improved by its combination with another NMR application, namely Magnetic Resonance Spectroscopy. The latter reveals information on the biochemical profile tissues, thereby allowing clinicians and radiologists to identify in a non{invasive way the different tissue types characterizing the sample under investigation, and to study the biochemical changes underlying a pathological situation. In particular, an NMR application exists which provides spatial as well as biochemical information. This application is called ...

Laudadio, Teresa — Katholieke Universiteit Leuven


Combining anatomical and spectral information to enhance MRSI resolution and quantification: Application to Multiple Sclerosis

Multiple sclerosis is a progressive autoimmune disease that a˙ects young adults. Magnetic resonance (MR) imaging has become an integral part in monitoring multiple sclerosis disease. Conventional MR imaging sequences such as fluid attenuated inversion recovery imaging have high spatial resolution, and can visualise the presence of focal white matter brain lesions in multiple sclerosis disease. Manual delineation of these lesions on conventional MR images is time consuming and su˙ers from intra and inter-rater variability. Among the advanced MR imaging techniques, MR spectroscopic imaging can o˙er complementary information on lesion characterisation compared to conventional MR images. However, MR spectroscopic images have low spatial resolution. Therefore, the aim of this thesis is to automatically segment multiple sclerosis lesions on conventional MR images and use the information from high-resolution conventional MR images to enhance the resolution of MR spectroscopic images. Automatic single time ...

Jain, Saurabh — KU Leuven


Least squares support vector machines classification applied to brain tumour recognition using magnetic resonance spectroscopy

Magnetic Resonance Spectroscopy (MRS) is a technique which has evolved rapidly over the past 15 years. It has been used specifically in the context of brain tumours and has shown very encouraging correlations between brain tumour type and spectral pattern. In vivo MRS enables the quantification of metabolite concentrations non-invasively, thereby avoiding serious risks to brain damage. While Magnetic Resonance Imaging (MRI) is commonly used for identifying the location and size of brain tumours, MRS complements it with the potential to provide detailed chemical information about metabolites present in the brain tissue and enable an early detection of abnormality. However, the introduction of MRS in clinical medicine has been difficult due to problems associated with the acquisition of in vivo MRS signals from living tissues at low magnetic fields acceptable for patients. The low signal-to-noise ratio makes accurate analysis of ...

Lukas, Lukas — Katholieke Universiteit Leuven


New approaches for EEG signal processing: Artifact EOG removal by ICA-RLS scheme and Tracks extraction method

Localizing the bioelectric phenomena originating from the cerebral cortex and evoked by auditory and somatosensory stimuli are clear objectives to both understand how the brain works and to recognize different pathologies. Diseases such as Parkinson's, Alzheimer's, schizophrenia and epilepsy are intensively studied to find a cure or accurate diagnosis. Epilepsy is considered the disease with major prevalence within disorders with neurological origin. The recurrent and sudden incidence of seizures can lead to dangerous and possibly life-threatening situations. Since disturbance of consciousness and sudden loss of motor control often occur without any warning, the ability to predict epileptic seizures would reduce patients' anxiety, thus considerably improving quality of life and safety. The common procedure for epilepsy seizure detection is based on brain activity monitorization via electroencephalogram (EEG) data. This process consumes a lot of time, especially in the case of long ...

Carlos Guerrero-Mosquera — University Carlos III of Madrid


Tissue Characterisation from Intravascular Ultrasound using Texture Analysis

Intravascular ultrasound has, over the past decade, significantly changed the clinical diagnosis and therapeutic strategy of coronary and vascular disease assessment, as it not only allows visualisation of the vessel lumen, but gives a unique view of the pathophysiologic structure of the artery wall. This information is currently unavailable from the universally accepted instrument for artery assessment, angiography, which has on several occasions had its diagnostic accuracy questioned. With intravascular ultrasound, there is the potential to categorise diseased arterial tissue belonging to distinct pathological groups which can ultimately aid in the understanding of individual lesions as well as making a significant contribution to treatment choice and management of cardiac patients. The high resolution image information offered by intravascular ultrasound provides excellent crosssectional views of coronary artery disease at the level of the disease process itself. This information can be used ...

Nailon, William Henry — University Of Edinburgh


Enhancement of Speech Signals - with a Focus on Voiced Speech Models

The topic of this thesis is speech enhancement with a focus on models of voiced speech. Speech is divided into two subcategories dependent on the characteristics of the signal. One part is the voiced speech, the other is the unvoiced. In this thesis, we primarily focus on the voiced speech parts and utilise the structure of the signal in relation to speech enhancement. The basis for the models is the harmonic model which is a very often used model for voiced speech because it describes periodic signals perfectly. First, we consider the problem of non-stationarity in the speech signal. The speech signal changes its characteristics continuously over time whereas most speech analysis and enhancement methods assume stationarity within 20-30 ms. We propose to change the model to allow the fundamental frequency to vary linearly over time by introducing a chirp ...

Nørholm, Sidsel Marie — Aalborg University


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


Automated quantification of preterm brain maturation using electroencephalography

Around 10 percent of all human births is premature, which means that annually about 15 million babies are born before 37 completed weeks of gestation. About one third of the admissions to the Neonatal Intensive Care Unit (NICU) consists of this patient group. Due to complications, 1 million babies die from premature delivery, and it is therefore the most important cause of neonatal death. In general, premature and immature babies have a high risk for neurological abnormalities by maturation in extra-uterine life. Even though improved health care has increased the survival changes of these neonates, they are sensitive to brain damage and consequently, neurocognitive disabilities. Nowadays, critical information about the brain development can be extracted from the electroencephalography (EEG). Clinical experts visually assess evolving EEG characteristics over both short and long periods to evaluate maturation of patients at risk and, ...

Koolen, Ninah — KU Leuven


New Approach to Dynamic Spectrum Management for DSL Environments

Currently, the telecommunications market has brought changes to the design of the old model of the telecommunications network. The emergence of new technologies for higher speed access was inevitable in order to meet the requirements of the appearance of the multimedia services (VoD, online gaming etc.). The latest technologies for broadband access over telephone pairs are Digital Subscriber Lines or DSL. This set of xDSL technologies allow the transfer of binary high speed over telephone twisted pair by using a suitable type of line codes. They allow a flow of high-speed information both asymmetrical and symmetrical over the telephone loop. This thesis presents the state of the art of Dynamic Spectrum Management (DSM) technologies suggested to improve the performance of DSL systems and proposes a new approach to this issue. The main contributions of this thesis includes extended bandwidth channel ...

Jakovljevic, Milos — Technical University of Madrid (UPM)


Adaptive Nonlocal Signal Restoration and Enhancement Techniques for High-Dimensional Data

The large number of practical applications involving digital images has motivated a significant interest towards restoration solutions that improve the visual quality of the data under the presence of various acquisition and compression artifacts. Digital images are the results of an acquisition process based on the measurement of a physical quantity of interest incident upon an imaging sensor over a specified period of time. The quantity of interest depends on the targeted imaging application. Common imaging sensors measure the number of photons impinging over a dense grid of photodetectors in order to produce an image similar to what is perceived by the human visual system. Different applications focus on the part of the electromagnetic spectrum not visible by the human visual system, and thus require different sensing technologies to form the image. In all cases, even with the advance of ...

Maggioni, Matteo — Tampere University of Technology


Glottal Source Estimation and Automatic Detection of Dysphonic Speakers

Among all the biomedical signals, speech is among the most complex ones since it is produced and received by humans. The extraction and the analysis of the information conveyed by this signal are the basis of many applications, including the topics discussed in this thesis: the estimation of the glottal source and the automatic detection of voice pathologies. In the first part of the thesis, after a presentation of existing methods for the estimation of the glottal source, a focus is made on the occurence of irregular glottal source estimations when the representation based on the Zeros of the Z-Transform (ZZT) is concerned. As this method is sensitive to the location of the analysis window, it is proposed to regularize the estimation by shifting the analysis window around its initial location. The best shift is found by using a dynamic ...

Dubuisson, Thomas — University of Mons


Sparse Modeling Heuristics for Parameter Estimation - Applications in Statistical Signal Processing

This thesis examines sparse statistical modeling on a range of applications in audio modeling, audio localizations, DNA sequencing, and spectroscopy. In the examined cases, the resulting estimation problems are computationally cumbersome, both as one often suffers from a lack of model order knowledge for this form of problems, but also due to the high dimensionality of the parameter spaces, which typically also yield optimization problems with numerous local minima. In this thesis, these problems are treated using sparse modeling heuristics, with the resulting criteria being solved using convex relaxations, inspired from disciplined convex programming ideas, to maintain tractability. The contributions to audio modeling and estimation focus on the estimation of the fundamental frequency of harmonically related sinusoidal signals, which is commonly used model for, e.g., voiced speech or tonal audio. We examine both the problems of estimating multiple audio sources ...

Adalbjörnsson, Stefan Ingi — Lund University


Signal processing and classification for magnetic resonance spectroscopic data with clinical applications

Over the last decades, Magnetic Resonance Imaging (MRI) has taken a leading role in the study of human body and it is widely used in clinical diagnosis. In vivo and ex vivo Magnetic Resonance Spectroscopic (MRS) techniques can additionally provide valuable metabolic information as compared to MRI and are gaining more clinical interest. The analysis of MRS data is a complex procedure and requires several preprocessing steps aiming to improve the quality of the data and to extract the most relevant features before any classification algorithm can be successfully applied. In this thesis a new approach to quantify magnetic resonance spectroscopic imaging (MRSI) data and therefore to obtain improved metabolite estimates is proposed. Then an important part is focusing on improving the diagnosis of glial brain tumors which are characterized by an extensive heterogeneity since various intramural histopathological properties such ...

Croitor Sava, Anca Ramona — KU Leuven

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