Recovering a linear combination of exponential signals characterized by parameters is highly significant in many MR imaging applications such as parameter mapping and spectroscopy. The parameters carry useful clinical information and can act as biomarkers for various cardiovascular and neurological disorders. However, their accurate estimation requires a large number of high spatial resolution images, resulting in long scan time. One of the ways to reduce scan time is by acquiring undersampled measurements. The recovery of images is usually posed as an optimization problem, which is regularized by functions enforcing sparsity, smoothness or low rank structure. Recently structured matrix priors have gained prominence in many MRI applications because of their superior performance over the aforementioned conventional priors. However, none of them are designed to exploit the smooth exponential structure of the 3D dataset. In this thesis, we exploit the exponential structure of the signal at every pixel location and the spatial smoothness of the parameters to derive a 3D annihilation relation in the Fourier domain. This relation translates into a product of a Hankel/Toeplitz structured matrix, formed from the k-t samples, and a vector of filter coefficients. We show that this matrix has a low rank structure, which is exploited to recover the images from undersampled measurements. We demonstrate the proposed method on the problem of MR parameter mapping. We compare the algorithm with the state-of-the-art methods and observe that the proposed reconstructions and parameter maps have fewer artifacts and errors. We extend the structured low rank framework to correct field inhomogeneity artifacts in MR images. We introduce novel approaches for field map compensation for data acquired using Cartesian and non-Cartesian trajectories. We adopt the time segmentation approach and reformulate the artifact correction problem into a recovery of time series of images from undersampled measurements. Upon recovery, the first image of the series will correspond to the distortion-free image. With the above re-formulation, we can assume that the signal at every pixel follows an exponential signal characterized by field map and the damping constant R2*. We exploit the smooth exponential structure of the 3D dataset to derive a low rank structured matrix prior, similar to the parameter mapping case. We demonstrate the algorithm on spherical MR phantom and human data and show that the artifacts are greatly reduced compared to the uncorrected images. Finally, we develop a structured matrix recovery framework to accelerate cardiac breath-held MRI. We model the cardiac image data as a 3D piecewise constant function. We assume that the zeros of a 3D trigonometric polynomial coincides with the edges of the image data, resulting in a Fourier domain annihilation relation. This relation can be compactly expressed in terms of a structured low rank matrix. We exploit this low rank property to recover the cardiac images from undersampled measurements. We demonstrate the superiority of the proposed technique over conventional sparsity and smoothness based methods. Though the model assumed here is not exponential, yet the proposed algorithm is closely related to that developed for parameter mapping. The direct implementation of the algorithms has a high memory demand and computational complexity due to the formation and storage of a large multi-fold Toeplitz matrix. Till date, the practical utility of such algorithms on high dimensional datasets has been limited due to the aforementioned reasons. We address these issues by introducing novel Fourier domain approximations which result in a fast and memory efficient algorithm for the above-mentioned applications. Such approximations allow us to work with large datasets efficiently and eliminate the need to store the Toeplitz matrix. We note that the algorithm developed for exponential recovery is general enough to be applied to other applications beyond MRI.

One of the most important challenges in dynamic magnetic resonance imaging (MRI) is to achieve high spatial and temporal resolution when it is limited by system performance. It is desirable to acquire data fast enough to capture the dynamics in the image time series without losing high spatial resolution and signal to noise ratio. Many techniques have been introduced in the recent decades to achieve this goal. Newly developed algorithms like Highly Constrained Backprojection (HYPR) and Compressed Sensing (CS) reconstruct images from highly undersampled data using constraints. Using these algorithms, it is possible to achieve high temporal resolution in the dynamic image time series with high spatial resolution and signal to noise ratio (SNR). In this thesis we have analyzed the performance of HYPR to CS algorithm. In assessing the reconstructed image quality, we considered computation time, spatial resolution, noise amplification factors, and artifact power (AP) using the same number of views in both algorithms, and that number is below the Nyquist requirement. In the simulations performed, CS always provides higher spatial resolution than HYPR, but it is limited by computation time in image reconstruction and SNR when compared to HYPR. HYPR performs better than CS in terms of SNR and computation time when the images are sparse enough. However, HYPR suffers from streaking artifacts when it comes to less sparse image data.

No description available.

Tissue engineering is limited by inability to create early and adequate blood supply. In-vivo DCE-MRI has imaged angiogenesis in soft tissues, yet has not been considered in hard tissues. Bilateral critical defects created in parietal bones of eighteen adult rabbits were left void, treated with haluronic acid acellular matrix (HA-ACM), or HA-ACM impregnated with vascular endothelial growth factor (VegF). DCE- MRI was acquired at weeks 1,2,3,6, and 12. Histologic analysis of HA-ACM treated defects demonstrated quantitatively greater immature bone formation, increased quantity and larger blood vessels compared to void. Statistically significant greater angiogenesis evidenced by quantitative perfusion on MRI supported histologic findings. DCE MRI is a novel means of imaging angiogenesis in grafted bone defects. DCE-MRI discerns physiologically important phases of angiogenesis: Initial vasoactive response, vessel network initiation, establishment, and pruning. DCE-MRI is adaptable to non-invasive study of candidate tissue engineered constructs and in evaluating scaffolds and treatments on angiogenesis.

Tissue engineering is limited by inability to create early and adequate blood supply. In-vivo DCE-MRI has imaged angiogenesis in soft tissues, yet has not been considered in hard tissues. Bilateral critical defects created in parietal bones of eighteen adult rabbits were left void, treated with haluronic acid acellular matrix (HA-ACM), or HA-ACM impregnated with vascular endothelial growth factor (VegF). DCE- MRI was acquired at weeks 1,2,3,6, and 12. Histologic analysis of HA-ACM treated defects demonstrated quantitatively greater immature bone formation, increased quantity and larger blood vessels compared to void. Statistically significant greater angiogenesis evidenced by quantitative perfusion on MRI supported histologic findings. DCE MRI is a novel means of imaging angiogenesis in grafted bone defects. DCE-MRI discerns physiologically important phases of angiogenesis: Initial vasoactive response, vessel network initiation, establishment, and pruning. DCE-MRI is adaptable to non-invasive study of candidate tissue engineered constructs and in evaluating scaffolds and treatments on angiogenesis.

<p>Living kidney donation is a clinical situation with unique features in the sense that healthy individuals voluntarily expose themselves to certain risks and inconveniences. Therefore, eliminating as much of the associated discomfort as possible is crucial. The primary aim of this study was to evaluate whether it is possible to use the examination with computed tomography (CT), which is essential to the investigation, also for determining the ratio of the two kidneys’ function – the split renal function. If possible, an examination with gamma camera renography could be excluded from the work-up. </p><p>To investigate this possibility, 27 subjects who had underwent CT and renography as part of kidney donor investigation were studied retrospectively. The quantity of contrast material in each kidney was considered proportional to that kidney’s function, and measurement was made in each of the two available contrast phases. The results were compared to the results from renography. A similar analysis was conducted in 38 patients investigated for suspected renal artery stenosis with CT and renography, including a study of an automatized method for the acquisition of data from CT. For further scrutiny, a respiratory triggered dynamic contrast-enhanced magnetic resonance imaging (MRI) examination was investigated in 26 individuals. Results of split renal function were compared with renography and with CT in a subgroup. To study the possibility of facilitating the data analysis with CT, a formula for approximation of the contrast attenuation was studied in 64 subjects. An analysis of the significance of choice of contrast phase was also conducted in 43 subjects. </p><p>Unsatisfactory agreement with renography resulted from the CT analysis of previous donors, partly due to technical shortcomings. However, the technique was recognized to have a potential value. In the subsequent material, the settings were improved, with beneficial effects on the agreement. Respiratory-triggered MRI generated high quality examinations of renal uptake and excretion, with results harmonizing well with renography and CT. The approximation formula applied to CT resulted in higher accuracy for renal volume assessment than with the automatic method, and an acceptable agreement of the split renal function estimate. </p><p>From the presented results, a revision of the current donor investigation protocol is suggested. CT gives sufficient information to exclude renography as a routine examination. In cases of uncertainty, renography is recommended for secondary evaluation.</p>

Living kidney donation is a clinical situation with unique features in the sense that healthy individuals voluntarily expose themselves to certain risks and inconveniences. Therefore, eliminating as much of the associated discomfort as possible is crucial. The primary aim of this study was to evaluate whether it is possible to use the examination with computed tomography (CT), which is essential to the investigation, also for determining the ratio of the two kidneys’ function – the split renal function. If possible, an examination with gamma camera renography could be excluded from the work-up. To investigate this possibility, 27 subjects who had underwent CT and renography as part of kidney donor investigation were studied retrospectively. The quantity of contrast material in each kidney was considered proportional to that kidney’s function, and measurement was made in each of the two available contrast phases. The results were compared to the results from renography. A similar analysis was conducted in 38 patients investigated for suspected renal artery stenosis with CT and renography, including a study of an automatized method for the acquisition of data from CT. For further scrutiny, a respiratory triggered dynamic contrast-enhanced magnetic resonance imaging (MRI) examination was investigated in 26 individuals. Results of split renal function were compared with renography and with CT in a subgroup. To study the possibility of facilitating the data analysis with CT, a formula for approximation of the contrast attenuation was studied in 64 subjects. An analysis of the significance of choice of contrast phase was also conducted in 43 subjects. Unsatisfactory agreement with renography resulted from the CT analysis of previous donors, partly due to technical shortcomings. However, the technique was recognized to have a potential value. In the subsequent material, the settings were improved, with beneficial effects on the agreement. Respiratory-triggered MRI generated high quality examinations of renal uptake and excretion, with results harmonizing well with renography and CT. The approximation formula applied to CT resulted in higher accuracy for renal volume assessment than with the automatic method, and an acceptable agreement of the split renal function estimate. From the presented results, a revision of the current donor investigation protocol is suggested. CT gives sufficient information to exclude renography as a routine examination. In cases of uncertainty, renography is recommended for secondary evaluation.

Cette thèse présente une méthodologie appliquée à la caractérisation de la dynamique de structures déformables sur des séquences temporelles (2D+t). Des indicateurs sont proposés pour estimer la mobilité de formes non-rigides, à partir de leurs contours. Deux approches complémentaires sont développées: En premier lieu, les descripteurs de forme sont utilisés pour quantifier les déformations globales des formes, et pour estimer des repères géométriques spécifiques. La deuxième approche repose sur l'appariement difféomorphique pour déterminer une paramétrisation unifiée des formes, afin de décrire les déformations. Une évaluation permet d'apprécier la qualité des indicateurs en termes de coût algorithmique, de robustesse face aux données altérées, et de capacité à différencier deux séquences.Cette approche de caractérisation est appliquée à des séquences IRM dynamiques de la cavité pelvienne, où les principaux organes pelviens (vessie, utérus-vagin, rectum) ont une grande variabilité morphologique, ils se déplacent et se déforment. Cette caractérisation est validée dans le cadre de deux applications. L'analyse statistique effectuée sur un ensemble de séquences permet de mettre en évidence des comportements caractéristiques des organes, d'identifier des références anatomiquement significatives, et d'aider à l'interprétation des diagnostics des organes. Aussi, dans le contexte de la réalisation d'une modélisation de la dynamique pelvienne patiente-spécifique, la caractérisation vise à évaluer quantitativement la précision de la modélisation, en utilisant l'IRM dynamique comme vérité-terrain. Ainsi, elle apporte des indications sur la correction des paramètres du modèle. / This thesis presents a methodology for the characterization of the dynamics of deformable structures on time-series data (2D+t). Some indicators are proposed in order to estimate non-rigid shape variations from their contours. Two complementary approaches are developed : First, shape descriptors are used to quantify the global deformations of the shapes, and to estimate specific geometric references. The second approach relies on the diffeomorphic mapping to determinate a unified parametrization of the shapes. Then, features are used to describe the deformations locally. Furthermore, the methodology has an evaluation step which consists in the assessment of the quality of the indicators in the algorithmic complexity, in the stability against data with a small variability, and in the ability to differentiate two sequences.The characterization is applied to dynamic MRI sequences of the pelvic cavity, where the main pelvic organs (bladder, uterus-vagina, rectum) have a high morphological variability, they undergo displacements and deformations. The characterization is validated within the context of two applications. Firslty, a statistical analysis is carried out on a set of sequences. It allows to highlight some properties of the organ behaviors, and to identify meaningful anatomical landmarks. The analysis helps also for the automatic interpretation of the organ diagnoses. Secondly, within the context of the development of a patient-specific pelvic dynamics modeling system, the characterization aims at assessing quantitatively the modeling precision. It uses the dynamic MRI as a ground truth. Thereby, it brings some clues about the correction of the model parameters.

Le Syndrome d’Apnée Obstructive du Sommeil affecte 4 à 6 % de la population en France soit près de 3 millions de personnes. Toutefois, les techniques de diagnostic usuelles ne permettent pas de déterminer de façon précise les sites d’occlusion ni de décrire les interactions fluide-paroi qui jouent un rôle important dans les processus de fermeture des voies aériennes supérieures. Au cours de ce travail, un ensemble d’outil a été mis en œuvre pour explorer les mécanismes sous-jacents conduisant à une apnée obstructive. La détermination géométrique et la caractérisation mécanique des voies aériennes supérieures, d’une part, la mesure des écoulements dans ces dernières, d’autre part, ont été réalisées par imagerie par résonance magnétique de l’hydrogène, pour les tissus, de l’hélium-3 et du fluor-19 pour les gaz. Les données obtenues ont été exploitées tout d’abord dans un modèle numérique statique pour estimer les lois d’état locales et caractériser la compliance des voies aériennes supérieures, puis, dans un modèle monodimensionnel, prenant en compte l’interaction fluide-structure et la limitation de débit au cours de l’inspiration, pour localiser les sites potentiellement responsables d’un éventuel collapsus. Par ailleurs, les écoulements de gaz d’hélium-3 et d’hexafluorure de soufre ont été simulés afin de déterminer le potentiel de ces deux modalités d’imagerie de gaz pour l’étude des obstructions des voies aériennes. La faisabilité d’une imagerie statique et dynamique par résonance magnétique du fluor a été démontrée. Avec une densité du gaz traceur bien plus importante, cette dernière technique présente une plus grande sensibilité à l’obstruction. Cette thèse ouvre ainsi une nouvelle voie de diagnostic et de guide thérapeutique personnalisé pour ce syndrome. / Obstructive Sleep Apnea (OSA) is a common disorder occurring in almost 3 million French people. However, current diagnosis methods are not sufficient to precisely define obstructing sites and doesn't take into account the fluid structure coupling which plays an important role during upper airway closing. During this thesis, we developed a series of tools exploring upper airway closing process. On the one hand, a screening tool of the structure and the mechanical properties of the upper airway, and on the other hand, a screening tool exploring with dynamic images of inert gases flow into the upper airway, were obtained using conventional hydrogen MRI coupled to magnetic resonance elastography (MRE) and helium-3 or fluor-19 gases MRI, respectively. Geometric and biomechanical data obtained using MRI/MRE are injected into a numerical model given the compliance and the state law of upper airway. Contributions of anatomical restriction on airway collapse are also investigated using a multi-compartmental two-dimensional fluid structure interaction model during a breath inspiration to predicted airway mechanical changes and collapse pressures. Furthermore, helium 3 and sulfur hexafluoride flow was modeled at steady state using commercial finite volume software to evaluate potential feasibility to image upper airway collapsibility during OSA. First dynamic MR imaging using sulfur hexafluoride (SF6) was obtained showing the feasibility of this technique. Using SF6, 6 times denser than air, shows a higher sensibility to upper airway obstruction. This thesis opens a new imaging modality to probe and to diagnose upper airway obstruction.

No description available.