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 ...

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 ...

In this thesis, the power of Machine Learning (ML) algorithms is combined with brain connectivity patterns, using Magnetic Resonance Imaging (MRI), for classification and prediction of Multiple Sclerosis (MS). White Matter (WM) as well as Grey Matter (GM) graphs are studied as connectome data types. The thesis addresses three main research objectives. The first objective aims to generate realistic brain connectomes data for improving the classification of MS clinical profiles in cases of data scarcity and class imbalance. To solve the problem of limited and imbalanced data, a Generative Adversarial Network (GAN) was developed for the generation of realistic and biologically meaningful connec- tomes. This network achieved a 10% better MS classification performance compared to classical approaches. As second research objective, we aim to improve classification of MS clinical profiles us- ing morphological features only extracted from GM brain tissue. ...

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 ...

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 ...

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 ...

Advances in wearable electrocardiogram (ECG) monitoring devices have allowed for new cardiovascular applications to emerge beyond diagnostics, such as stress and fatigue detection, athletic performance assessment, sleep disorder characterization, mood recognition, activity surveillance, biometrics, and fitness tracking, to name a few. Such devices, however, are prone to artifacts, particularly due to movement, thus hampering heart rate and heart rate variability measurement and posing a serious threat to cardiac monitoring applications. To address these issues, this thesis proposes the use of a spectro-temporal signal representation called “modulation spectrum”, which is shown to accurately separate cardiac and noise components from the ECG signals, thus opening doors for noise-robust ECG signal processing tools and applications. First, an innovative ECG quality index based on the modulation spectral signal representation is proposed. The representation quantifies the rate-of-change of ECG spectral components, which are shown to ...

Diffusion Magnetic Resonance Imaging (dMRI) is a meaningful technique for white matter (WM) fiber-tracking and microstructural characterization of axonal/neuronal integrity and connectivity. By measuring water molecules motion in the three directions of space, numerous parametric maps can be reconstructed. Among these, fractional anisotropy (FA), mean diffusivity (MD), and axial (λa) and radial (λr) diffusivities have extensively been used to investigate brain diseases. Overall, these findings demonstrated that WM and grey matter (GM) tissues are subjected to numerous microstructural alterations in multiple sclerosis (MS). However, it remains unclear whether these tissue alterations result from global processes, such as inflammatory cascades and/or neurodegenerative mechanisms, or local inflammatory and/or demyelinating lesions. Furthermore, these pathological events may occur along afferent or afferent WM fiber pathways, leading to antero- or retrograde degeneration. Thus, for a better understanding of MS pathological processes like its spatial and ...

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 ...

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 ...

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.

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 ...

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 ...

Obstructive sleep apnea (OSA) is among the most prevalent sleep disorders, which is estimated to affect 6 %−19 % of women and 13 %−33 % of men. Besides daytime sleepiness, impaired cognitive functioning and an increased risk for accidents, OSA may lead to obesity, diabetes and cardiovascular diseases (CVD) on the long term. Its prevalence is only expected to rise, as it is linked to aging and excessive body fat. Nevertheless, many patients remain undiagnosed and untreated due to the cumbersome clinical diagnostic procedures. For this, the patient is required to sleep with an extensive set of body attached sensors. In addition, the recordings only provide a single night perspective on the patient in an uncomfortable, and often unknown, environment. Thus, large scale monitoring at home is desired with comfortable sensors, which can stay in place for several nights. To ...

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 ...