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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

Over the past years magnetic resonance spectroscopy (MRS) has been of significant importance both as a fundamental research technique in different fields, as well as a diagnostic tool in medical environments. With MRS, for example, spectroscopic information, such as the concentrations of chemical substances, can be determined non-invasively. To that end, the signals are first modeled by an appropriate model function and mathematical techniques are subsequently applied to determine the model parameters. In this thesis, signal processing algorithms are developed to quantify in-vivo and ex-vivo MRS signals. These are usually characterized by a poor signal-to-noise ratio, overlapping peaks, deviations from the model function and in some cases the presence of disturbing components (e.g. the residual water in proton spectra). The work presented in this thesis addresses a part of the total effort to provide accurate, efficient and automatic data analysis ...

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.

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 ...

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 ...

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 ...