Integration of anatomical and hemodynamical information in magnetic resonance angiography

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Ultra-high-resolution 3D imaging of atherosclerosis in mice with synchrotron differential phase contrast: a proof of concept study.

The goal of this study was to investigate the performance of 3D synchrotron differential phase contrast (DPC) imaging for the visualization of both macroscopic and microscopic aspects of atherosclerosis in the mouse vasculature ex vivo. The hearts and aortas of 2 atherosclerotic and 2 wild-type control mice were scanned with DPC imaging with an isotropic resolution of 15 μm. The coronary artery vessel walls were segmented in the DPC datasets to assess their thickness, and histological staining was performed at the level of atherosclerotic plaques. The DPC imaging allowed for the visualization of complex structures such as the coronary arteries and their branches, the thin fibrous cap of atherosclerotic plaques as well as the chordae tendineae. The coronary vessel wall thickness ranged from 37.4 ± 5.6 μm in proximal coronary arteries to 13.6 ± 3.3 μm in distal branches. No consistent differences in coronary vessel wall thickness were detected between the wild-type and atherosclerotic hearts in this proof-of-concept study, although the standard deviation in the atherosclerotic mice was higher in most segments, consistent with the observation of occasional focal vessel wall thickening. Overall, DPC imaging of the cardiovascular system of the mice allowed for a simultaneous detailed 3D morphological assessment of both large structures and microscopic details

New Advances in Susceptibility Weighted MRI to Determine Physiological Parameters

Die Magnetresonanztomographie bietet die Möglichkeit der Bestimmung des Blutoxygenierungsgrades kleiner venöser Gefäße und damit lokaler Hirnareale mit Hilfe einer Multiecho-Gradientenecho-Sequenz. Mit dieser Sequenz kann der Signalzerfall in einem Voxel, welches von einer einzelnen Vene bzw. von Blutkapillaren durchzogen ist, bestimmt werden. Der Signalzerfall ist charakteristisch für die von der Vene oder den Kapillaren erzeugten Feldinhomogenitäten, so dass sich Aussagen über den Blutoxygenierungsgrad und Blutvolumenanteil treffen lassen. Durch Fitten simulierter Signalverläufe an gemessene Phantom- und Probandendaten konnte gezeigt werden, dass es mit der hier vorgestellten Methode möglich ist, den venösen Blutoxygenierungsgrad zu quantifizieren. Weiterhin konnte eine durch gezielte Modulation des zerebralen Blutflusses hervorgerufene Änderung der Blutoxygenierung in vivo nachgewiesen werden. Die Erweiterung des Modells eines einzelnen Gefäßes auf ein Gefäßnetzwerk diente als Grundlage zur theoretischen Beschreibung der Blutkapillaren, die das Hirngewebe durchziehen und mit Sauerstoff versorgen. Dieses Netzwerkmodel konnte in Phantomexperimenten verifiziert werden. Dagegen zeigte sich bei einer Probandenmessung, dass es nicht möglich ist einzig anhand des gemessenen Signalverlaufs valide Werte für die Blutoxygenierung und den Blutvolumenanteil eindeutig zu bestimmen. Die hohe Korrelation zwischen beiden Parametern bewirkt, dass mehrere Paare von Oxygenierungs- und Volumenwerten passende Signalkurven liefern. Eine unabhängige Quantifizierung oder Abschätzung des venösen Blutvolumens kann hier helfen eindeutige Oxygenierungswerte zu erhalten. Im Rahmen der vorliegenden Dissertation konnte das Signalverhalten von suszeptibilitätssensitiven Messungen in der Magnetresonanztomographie genauer untersucht und eine Methode zur nicht-invasiven Bestimmung der venösen Blutoxygenierung an einzelnen Gefäßen entwickelt werden. Erste in vivo Ergebnisse des Gefäßnetzwerkes verdeutlichen, dass für eine genaue Quantifizierung der Blutoxygenierung weitere Parameter, wie das Blutvolumen, unabhängig bestimmt werden müssen. Dennoch ist es möglich, die Methode am einzelnen Blutgefäß zur besseren Charakterisierung von Pathologien sowie physiologischen Änderungen, z.B. bei der funktionellen Magnetresonanztomographie, einzusetzen.Magnetic resonance imaging allows to determine the blood oxygenation level of small venous vessels or the blood capillary network by evaluating the magnetic resonance signal acquired with multi-echo gradient-echo sequences. The signal formation of a voxel traversed by a vein or interspersed with capillaries shows a characteristic decay or modulation as a function of time from which the blood oxygenation and blood volume fraction can be derived. It could be demonstrated in phantom measurements that the signal of a single vessel traversed voxel correctly matched the calculations of numerical signal simulation. By fitting the signal simulation to in vivo measurements of cerebral venous vessels, vessel size and venous blood oxygenation was determined quantitatively. Furthermore, it was possible to detect and to quantify a physiologically induced change in cerebral venous blood oxygenation. To describe the signal of the blood capillary network in normal brain matter, an extension of the single vessel model to a vessel network was applied. This network model was also validated in phantom experiments. As a result of these investigations it was found that the two parameters describing the network, the blood volume fraction and blood oxygenation level, are correlated to each other and can not be separated without additional information by simply fitting the signal simulation to the measurement. This finding was of special importance in the initial in vivo measurements conducted in the present work. Where, independent blood volume determination may help to further validate the quantified blood oxygenation level. In the present work a non-invasive method was developed to quantify cerebral blood oxygenation levels in single veins. This was possible by investigating the signal evolution of susceptibility sensitive magnetic resonance imaging. The initial result of the vessel network signal reveals, that for obtaining a valid blood oxygenation level, the volume fraction has to be further determined by an independent measurement. Nevertheless, is has been demonstrated that the quantification of the blood oxygenation level in single venous vessels is possible and can be applied in clinical diagnosis for better characterization of cerebral pathologies or in physiological investigations, like in functional magnetic resonance imaging

Feasibility of in vivo measurement of carotid wall shear rate using spiral Fourier velocity encoded MRI

Arterial wall shear stress is widely believed to influence the formation and growth of atherosclerotic plaque; however, there is currently no gold standard for its in vivo measurement. The use of phase contrast MRI has proved to be challenging due to partial-volume effects and inadequate signal-to-noise ratio at the high spatial resolutions that are required. This work evaluates the use of spiral Fourier velocity encoded MRI as a rapid method for assessing wall shear rate in the carotid arteries. Wall shear rate is calculated from velocity histograms in voxels spanning the blood/vessel wall interface, using a method developed by Frayne and Rutt (Magn Reson Med 1995;34:378–387). This study (i) demonstrates the accuracy of the velocity histograms measured by spiral Fourier velocity encoding in a pulsatile carotid flow phantom compared with high-resolution two-dimensional Fourier transform phase contrast, (ii) demonstrates the accuracy of Fourier velocity encoding–based shear rate measurements in a numerical phantom designed using a computational fluid dynamics simulation of carotid flow, and (iii) demonstrates in vivo measurement of regional wall shear rate and oscillatory shear index in the carotid arteries of healthy volunteers at 3 T. Magn Reson Med 63:1537–1547, 2010. © 2010 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75777/1/22325_ftp.pd

Caractérisation géométrique par la logique floue et simulation de la résorption cellulairement assistée de substituts poreux pour tissus osseux par microtomographie à rayons X

The objective of this thesis is to provide an improved characterization of porous scaffolds. A more focused objective is to provide a computational model simulating the cell mediated resorption process of resorbable bone substitutes. The thesis is structured in three scientific manuscripts. The first manuscript used fuzzy-based image treatment methods to analyse images generated by micro-computed tomography. From the literature, it is known that the fuzzy-based method helps to improve the accuracy of the characterization, in particular for scaffolds featuring a relatively small pore size. In addition, a new algorithm was introduced to determine both pore and interconnection sizes. The surface area of bone substitutes was quantified by using marching cube algorithm. Besides, the so-called Lattice Boltzmann method was used to characterize the permeability of the investigated scaffolds. Scaffolds made of [béta]-tricalcium phosphate ([béta]-Ca[subscript 3](PO[subscript 4])[subscript 2]) and presenting a constant porosity and four variable pore sizes were examined. The average pore size (diameter) of the four bone substitute groups (denominated with a letter from group A to D) was measured to be 170.3«1.7, 217.3«5.2, 415.8«18.8 and 972.3«10.9 [micro]m. Despite this significant change in pore size, the pore interconnection size only increased slightly, in the range of 61.7 to 85.2 [micro]m. The average porosity of the four groups was 52.3«1.5 %. The surface density of scaffolds decreased from 11.5 to 3.3 mm[superscript -1], when the pore size increased. The results revealed that the permeability of scaffolds is in the same order of magnitude and increased from 1.1?10[superscript -10] to 4.1?10[superscript -10] m[superscript 2] with increasing the pore size. The second manuscript was devoted to the use of subvoxelization algorithm and high-resolution scanner, in an attempt to further improve the accuracy of the results, in particular, of the small pore scaffolds. As expected, an increase of the image resolution from 15 to 7.5 [micro]m significantly eased the segmentation process and hence improved scaffold characterization. Subvoxelization also improved the results specifically in terms of interconnection sizes. Specifically, much smaller interconnection sizes were yielded after applying the subvoxelization process. For example, the mean interconnection size of small pore size groups, group A and B, dropped from 63 to 20 and 30 [micro]m, respectively. Furthermore, due to more details obtained from subvoxelization and high-resolution scanning, additional effects so called"boundary effects" were observed. The boundary effects can yield misleading results in terms of interconnection sizes. The means to reduce these effects were proposed. The third manuscript focused on the simulation and understanding of cell mediated resorption of bone graft substitutes. A computer model was developed to simulate the resorption process of four bone substitute groups. [mu]CT data and new"image processing" tools such as labelling and skeletonization were combined in an algorithm to perform the steps of resorption simulation algorithm. The proposed algorithm was verified by comparing simulation results with the analytical results of a simple geometry and biological in vivo data of bone substitutes. A correlation coefficient between the simulation results and both analytical and experimental data, was found to be larger than 0.9. Local resorption process revealed faster resorption in external region specifically at earlier resorption time. This finding is in agreement with the in vivo results. Two definitions were introduced to estimate the resorption rate; volume resorption rate and linear resorption rate. The volume resorption rate was proportional to accessible surface and decreased when the pore size increased, while the linear resorption rate was proportional to thickness of material and increased with increasing the pore size. In addition, the simulation results revealed no effect of resorption direction on resorption behaviour of substitutes. However, the resorption rate of small pore size samples was decreased with increasing the minimum interconnection size required for cell ingrowth, to 100 [micro]m. This thesis combined novel"image processing" tools and subvoxelization method to improve the characterization of porous bone substitutes used in the bone repair process. The improved characterization allowed a more accurate simulation process. The simulation data were consistent with previously obtained biological data of the same group and allows understanding the local resorption process. The available tools and results are expected to help with the design of optimal substitute for bone repair."--Résumé abrégé par UMI

Experimental MRI monitoring of renal blood volume fraction variations en route to renal magnetic resonance oximetry

Diagnosis of early-stage acute kidney injury (AKI) will benefit from a timely identification of local tissue hypoxia. Renal tissue hypoxia is an early feature in AKI pathophysiology, and renal oxygenation is increasingly being assessed through T(2)*-weighted magnetic resonance imaging (MRI). However, changes in renal blood volume fraction (BVf) confound renal T(2)*. The aim of this study was to assess the feasibility of intravascular contrast-enhanced MRI for monitoring renal BVf during physiological interventions that are concomitant with variations in BVf and to explore the possibility of correcting renal T(2)* for BVf variations. A dose-dependent study of the contrast agent ferumoxytol was performed in rats. BVf was monitored throughout short-term occlusion of the renal vein, which is known to markedly change renal blood partial pressure of O(2) and BVf. BVf calculated from MRI measurements was used to estimate oxygen saturation of hemoglobin (SO(2)). BVf and SO(2) were benchmarked against cortical data derived from near-infrared spectroscopy. As estimated from magnetic resonance parametric maps of T(2) and T(2)*, BVf was shown to increase, whereas SO(2) was shown to decline during venous occlusion (VO). This observation could be quantitatively reproduced in test-retest scenarios. Changes in BVf and SO(2) were in good agreement with data obtained from near-infrared spectroscopy. Our findings provide motivation to advance multiparametric MRI for studying AKIs, with the ultimate goal of translating MRI-based renal BVf mapping into clinical practice en route noninvasive renal magnetic resonance oximetry as a method of assessing AKI and progression to chronic damage

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus