Magnetic Resonance Spectroscopy (MRS) is a technique used in fundamental research and in clinical environments. During recent years, clinical application of MRS gained importance, especially as a non-invasive tool for diagnosis and therapy monitoring of brain and prostate tumours. The most important asset of MRS is its ability to determine the concentration of chemical substances non-invasively. To extract relevant signal parameters, MRS data have to be quantified. This usually doesn¢t prove to be straightforward since in vivo MRS signals are characterized by poor signal-to-noise ratios, overlapping peaks, acquisition related artefacts and the presence of disturbing components (e.g. residual water in proton spectra). The work presented in this thesis aims to improve the quantification in different applications of MRS in vivo. To obtain the signal parameters related to MRS data, different approaches were suggested in the past. Black-box methods, don¢t require ...

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 ...

Assertive diagnosis of cancer, Alzheimer’s disease, epilepsy and other metabolic diseases is essential to provide patients with the adequate treatment. Recently, different invasive and non-invasive techniques have been developed for this purpose, nevertheless, due to their harmless properties the non-invasive techniques have gained more value. Magnetic Resonance is a well-known non-invasive technique that provides spectra (metabolite peaks) and images (anatomical structures) of the examined tissue. In Magnetic Resonance Spectroscopy (MRS), molecules containing certain excitable nuclei, such as 1H, provide the metabolite information. As a consequence, the peaks in the MR spectra correspond to observable metabolites which are the biomarkers of diseases. Finally, metabolite concentrations are computed and compared against normal values in order to establish the diagnosis. The method to obtain such amplitudes is also called quantification and its accuracy is essential for diagnosis assessment. Quantification of MRS signals is ...

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 ...

Nowadays, diagnosis and treatment of brain tumors is based on clinical symptoms, radiological appearance, and often histopathology. Magnetic resonance imaging (MRI) is a major noninvasive tool for the anatomical assessment of tumors in the brain. However, several diagnostic questions, such as the type and grade of the tumor, are difficult to address using MRI. The histopathology of a tissue specimen remains the gold standard, despite the associated risks of surgery to obtain a biopsy. In recent years, the use of magnetic resonance spectroscopy (MRS), which provides a metabolic profile, has gained a lot of interest for a more detailed and specific noninvasive evaluation of brain tumors. In particular, magnetic resonance spectroscopic imaging (MRSI) is attractive as this may also enable to visualize the heterogeneous spatial extent of tumors, both inside and outside the MRI detectable lesion. As manual, individual, viewing ...

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 ...

Recent advances in many fields ranging from engineering to natural science, require increasingly complicated optimization tasks in the experiment design, for which the target objectives are generally in the form of black-box functions that are expensive to evaluate. In a common formulation of this problem, a designer is expected to solve the black-box optimization tasks via sequentially attempting candidate solutions and receiving feedback from the system. This thesis considers Bayesian optimization (BO) as the black-box optimization framework, and investigates the enhancements on BO from the aspects of efficiency, adaptation and reliability. Generally, BO consists of a surrogate model for providing probabilistic inference and an acquisition function which leverages the probabilistic inference for selecting the next candidate solution. Gaussian process (GP) is a prominent non-parametric surrogate model, and the quality of its inference is a critical factor on the optimality performance ...

The medical diagnosis of brain tumours is one of the main applications of Magnetic Resonance. Magnetic Resonance consists of two main branches: Imaging and Spectroscopy. Magnetic Resonance Imaging is very well-known as the radiologic technique applied to produce high-quality images of tissues, such as the brain tissue, for diagnostic purposes. Magnetic Resonance Spectroscopy provides chemical information about all the molecules present in the brain, such as their concentrations. Both Imaging and Spectroscopy can be exploited for the grading and typing of brain tumours, also called the classification of brain tumours. As first topic, this thesis mainly studied the contribution of Spectroscopy for automated classification and the influence of several factors on the classification performance. It was found that a few preprocessing steps did not have a large impact on the classification results. This implies that several preprocessing steps can be ...

Magnetic Resonance Spectroscopy has been successfully used in brain tumor diagnosis and represents a complementary aid to the well-known technique, Magnetic Resonance Imaging, by providing metabolic information that is not available with the latter. Both Imaging and Spectroscopy can be used for the grading and typing of brain tumors. Classifying brain tumors from spectroscopic data is not trivial and requires several steps. The common main steps are preprocessing, feature extraction and, finally, classification of the data. The preprocessing step aims to clean up the data and to normalize them in order to facilitate the extraction of the relevant features. These features, once selected and extracted, are used in a classifier, whose output is a brain tumor class. The challenge is to improve brain tumor diagnosis based on spectroscopic data. In this thesis, we analyzed methods used in each of the ...

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 ...

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.

This thesis focuses on the development of automatic accompaniment sys- tems. We investigate previous systems and look at a range of approaches that have been attempted for the problem of beat tracking. Most beat trackers are intended for the purposes of music information retrieval where a ‘black box’ approach is tested on a wide variety of music genres. We highlight some of the difficulties facing offline beat trackers and design a new approach for the problem of real-time drum tracking, developing a system, B-Keeper, which makes reasonable assumptions on the nature of the signal and is provided with useful prior knowledge. Having developed the system with offline studio recordings, we look to test the system with human players. Existing offline evaluation methods seem less suitable for a performance system, since we also wish to evaluate the interaction between musician and ...

To reduce scanning time or improve spatio-temporal resolution in some MRI applications, parallel MRI acquisition techniques with multiple coils have emerged since the early 90’s as powerful methods. In these techniques, MRI images have to be reconstructed from ac- quired undersampled “k-space” data. To this end, several reconstruction techniques have been proposed such as the widely-used SENSitivity Encoding (SENSE) method. However, the reconstructed images generally present artifacts due to the noise corrupting the ob- served data and coil sensitivity profile estimation errors. In this work, we present novel SENSE-based reconstruction methods which proceed with regularization in the complex wavelet domain so as to promote the sparsity of the solution. These methods achieve ac- curate image reconstruction under degraded experimental conditions, in which neither the SENSE method nor standard regularized methods (e.g. Tikhonov) give convincing results. The proposed approaches relies on ...

In an automotive environment, quality of speech communication using a hands-free equipment is often deteriorated by interfering car noise. In order to preserve the speech signal without car noise, a multichannel speech enhancement system including a beamformer and a post-filter can be applied. Since employing a beamformer alone is insufficient to substantially reducing the level of car noise, a post-filter has to be applied to provide further noise reduction, especially at low frequencies. In this thesis, two novel post-filter designs along with their optimization for different driving conditions are presented. The first post-filter design utilizes an adaptive smoothing factor for the power spectral density estimation as well as a hybrid noise coherence function. The hybrid noise coherence function is a mixture of the diffuse and the measured noise coherence functions for a specific driving condition. The second post-filter design applies ...

Magnetic Resonance Imaging (MRI) is an important diagnostic tool for imaging soft tissue without the use of ionizing radiation. Moreover, through advanced signal processing, MRI can provide more than just anatomical information, such as estimates of tissue-specific physical properties. Signal processing lies at the very core of the MRI process, which involves input design, information encoding, image reconstruction, and advanced filtering. Based on signal modeling and estimation, it is possible to further improve the images, reduce artifacts, mitigate noise, and obtain quantitative tissue information. In quantitative MRI, different physical quantities are estimated from a set of collected images. The optimization problems solved are typically nonlinear, and require intelligent and application-specific algorithms to avoid suboptimal local minima. This thesis presents several methods for efficiently solving different parameter estimation problems in MRI, such as multi-component T2 relaxometry, temporal phase correction of complex-valued ...