Flow pattern analysis for magnetic resonance velocity imaging

Blood flow in the heart is highly complex. Although blood flow patterns have been investigated by both computational modelling and invasive/non-invasive imaging techniques, their evolution and intrinsic connection with cardiovascular disease has yet to be explored. Magnetic resonance (MR) velocity imaging provides a comprehensive distribution of multi-directional in vivo flow distribution so that detailed quantitative analysis of flow patterns is now possible. However, direct visualisation or quantification of vector fields is of little clinical use, especially for inter-subject or serial comparison of changes in flow patterns due to the progression of the disease or in response to therapeutic measures. In order to achieve a comprehensive and integrated description of flow in health and disease, it is necessary to characterise and model both normal and abnormal flows and their effects. To accommodate the diversity of flow patterns in relation to morphological and functional changes, we have described in this thesis an approach of detecting salient topological features prior to analytical assessment of dynamical indices of the flow patterns. To improve the accuracy of quantitative analysis of the evolution of topological flow features, it is essential to restore the original flow fields so that critical points associated with salient flow features can be more reliably detected. We propose a novel framework for the restoration, abstraction, extraction and tracking of flow features such that their dynamic indices can be accurately tracked and quantified. The restoration method is formulated as a constrained optimisation problem to remove the effects of noise and to improve the consistency of the MR velocity data. A computational scheme is derived from the First Order Lagrangian Method for solving the optimisation problem. After restoration, flow abstraction is applied to partition the entire flow field into clusters, each of which is represented by a local linear expansion of its velocity components. This process not only greatly reduces the amount of data required to encode the velocity distribution but also permits an analytical representation of the flow field from which critical points associated with salient flow features can be accurately extracted. After the critical points are extracted, phase portrait theory can be applied to separate them into attracting/repelling focuses, attracting/repelling nodes, planar vortex, or saddle. In this thesis, we have focused on vortical flow features formed in diastole. To track the movement of the vortices within a cardiac cycle, a tracking algorithm based on relaxation labelling is employed. The constraints and parameters used in the tracking algorithm are designed using the characteristics of the vortices. The proposed framework is validated with both simulated and in vivo data acquired from patients with sequential MR examination following myocardial infarction. The main contribution of the thesis is in the new vector field restoration and flow feature abstraction method proposed. They allow the accurate tracking and quantification of dynamic indices associated with salient features so that inter- and intra-subject comparisons can be more easily made. This provides further insight into the evolution of blood flow patterns and permits the establishment of links between blood flow patterns and localised genesis and progression of cardiovascular disease.Open acces

Illustrative Flow Visualization of 4D PC-MRI Blood Flow and CFD Data

Das zentrale Thema dieser Dissertation ist die Anwendung illustrativer Methoden auf zwei bisher ungelöste Probleme der Strömungsvisualisierung. Das Ziel der Strömungsvisualisierung ist die Bereitstellung von Software, die Experten beim Auswerten ihrer Strömungsdaten und damit beim Erkenntnisgewinn unterstützt. Bei der illustrativen Visualisierung handelt es sich um einen Zweig der Visualisierung, der sich an der künstlerischen Arbeit von Illustratoren orientiert. Letztere sind darauf spezialisiert komplizierte Zusammenhänge verständlich und ansprechend zu vermitteln. Die angewendeten Techniken werden in der illustrativen Visualisierung auf reale Daten übertragen, um die Effektivität der Darstellung zu erhöhen. Das erste Problem, das im Rahmen dieser Dissertation bearbeitet wurde, ist die eingeschränkte Verständlichkeit von komplexen Stromflächen. Selbstverdeckungen oder Aufrollungen behindern die Form- und Strömungswahrnehmung und machen diese Flächen gerade in interessanten Strömungssituationen wenig nützlich. Auf Basis von handgezeichneten Strömungsdarstellungen haben wir ein Flächenrendering entwickelt, das Silhouetten, nicht-photorealistische Beleuchtung und illustrative Stromlinien verwendet. Interaktive Flächenschnitte erlauben die Exploration der Flächen und der Strömungen, die sie repräsentieren. Angewendet auf verschiedene Stromflächen ließ sich zeigen, dass die Methoden die Verständlichkeit erhöhen, v.a. in Bereichen komplexer Strömung mit Aufwicklungen oder Singularitäten. Das zweite Problem ist die Strömungsanalyse des Blutes aus 4D PC-MRI-Daten. An diese relativ neue Datenmodalität werden hohe Erwartungen für die Erforschung und Behandlung kardiovaskulärer Krankheiten geknüpft, da sie erstmals ein dreidimensionales, zeitlich aufgelöstes Abbild der Hämodynamik liefert. Bisher werden 4D PC-MRI-Daten meist mit Werkzeugen der klassischen Strömungsvisualisierung verarbeitet. Diese werden den besonderen Ansprüchen der medizinischen Anwender jedoch nicht gerecht, die in kurzer Zeit eine übersichtliche Darstellung der relevanten Strömungsaspekte erhalten möchten. Wir haben ein Werkzeug zur visuellen Analyse der Blutströmung entwickelt, welches eine einfache Detektion von markanten Strömungsmustern erlaubt, wie z.B. Jets, Wirbel oder Bereiche mit hoher Blutverweildauer. Die Grundidee ist hierbei aus vorberechneten Integrallinien mit Hilfe speziell definierter Linienprädikate die relevanten, d.h. am gefragten Strömungsmuster, beteiligten Linien ausgewählt werden. Um eine intuitive Darstellung der Resultate zu erreichen, haben wir uns von Blutflußillustrationen inspirieren lassen und präsentieren eine abstrakte Linienbündel- und Wirbeldarstellung. Die Linienprädikatmethode sowie die abstrakte Darstellung der Strömungsmuster wurden an 4D PC-MRI-Daten von gesunden und pathologischen Aorten- und Herzdaten erfolgreich getestet. Auch die Evaluierung durch Experten zeigt die Nützlichkeit der Methode und ihr Potential für den Einsatz in der Forschung und der Klinik.This thesis’ central theme is the use of illustrative methods to solve flow visualization problems. The goal of flow visualization is to provide users with software tools supporting them analyzing and extracting knowledge from their fluid dynamics data. This fluid dynamics data is produced in large amounts by simulations or measurements to answer diverse questions in application fields like engineering or medicine. This thesis deals with two unsolved problems in flow visualization and tackles them with methods of illustrative visualization. The latter is a subbranch of visualization whose methods are inspired by the art work of professional illustrators. They are specialized in the comprehensible and esthetic representation of complex knowledge. With illustrative visualization, their techniques are applied to real data to enhance their representation. The first problem dealt with in this thesis is the limited shape and flow perception of complex stream surfaces. Self-occlusion and wrap-ups hinder their effective use in the most interesting flow situations. On the basis of hand-drawn flow illustrations, a surface rendering method was designed that uses silhouettes, non-photorealistic shading, and illustrative surface stream lines. Additionally, geometrical and flow-based surface cuts allow the user an interactive exploration of the surface and the flow it represents. By applying this illustrative technique to various stream surfaces and collecting expert feedback, we could show that the comprehensibility of the stream surfaces was enhanced – especially in complex areas with surface wrap-ups and singularities. The second problem tackled in this thesis is the analysis of blood flow from 4D PC-MRI data. From this rather young data modality, medical experts expect many advances in the research of cardiovascular diseases because it delivers a three-dimensional and time-resolved image of the hemodynamics. However, 4D PC-MRI data are mainly processed with standard flow visualizaton tools, which do not fulfill the requirements of medical users. They need a quick and easy-to-understand display of the relevant blood flow aspects. We developed a tool for the visual analysis of blood flow that allows a fast detection of distinctive flow patterns, such as high-velocity jets, vortices, or areas with high residence times. The basic idea is to precalculate integral lines and use specifically designed line predicates to select and display only lines involved in the pattern of interest. Traditional blood flow illustrations inspired us to an abstract and comprehensible depiction of the resulting line bundles and vortices. The line predicate method and the illustrative flow pattern representation were successfully tested with 4D PC-MRI data of healthy and pathological aortae and hearts. Also, the feedback of several medical experts confirmed the usefulness of our methods and their capabilities for a future application in the clinical research and routine

On motion in dynamic magnetic resonance imaging: Applications in cardiac function and abdominal diffusion

La imagen por resonancia magnética (MRI), hoy en día, representa una potente herramienta para el diagnóstico clínico debido a su flexibilidad y sensibilidad a un amplio rango de propiedades del tejido. Sus principales ventajas son su sobresaliente versatilidad y su capacidad para proporcionar alto contraste entre tejidos blandos. Gracias a esa versatilidad, la MRI se puede emplear para observar diferentes fenómenos físicos dentro del cuerpo humano combinando distintos tipos de pulsos dentro de la secuencia. Esto ha permitido crear distintas modalidades con múltiples aplicaciones tanto biológicas como clínicas. La adquisición de MR es, sin embargo, un proceso lento, lo que conlleva una solución de compromiso entre resolución y tiempo de adquisición (Lima da Cruz, 2016; Royuela-del Val, 2017). Debido a esto, la presencia de movimiento fisiológico durante la adquisición puede conllevar una grave degradación de la calidad de imagen, así como un incremento del tiempo de adquisición, aumentando así tambien la incomodidad del paciente. Esta limitación práctica representa un gran obstáculo para la viabilidad clínica de la MRI. En esta Tesis Doctoral se abordan dos problemas de interés en el campo de la MRI en los que el movimiento fisiológico tiene un papel protagonista. Éstos son, por un lado, la estimación robusta de parámetros de rotación y esfuerzo miocárdico a partir de imágenes de MR-Tagging dinámica para el diagnóstico y clasificación de cardiomiopatías y, por otro, la reconstrucción de mapas del coeficiente de difusión aparente (ADC) a alta resolución y con alta relación señal a ruido (SNR) a partir de adquisiciones de imagen ponderada en difusión (DWI) multiparamétrica en el hígado.Departamento de Teoría de la Señal y Comunicaciones e Ingeniería TelemáticaDoctorado en Tecnologías de la Información y las Telecomunicacione

The ring vortex complex flow phantom: characterisation, optimisation and expansion

The field of cardiovascular diagnostic imaging is rapidly evolving, with emerging state-of-the-art medical flow visualisation technologies demonstrating superior quantitative abilities. These techniques require rigorous QA through flow phantoms which generate well-characterised and challenging flows, a requirement not met by current flow test objects. The ring vortex complex flow phantom is a prototype device designed and manufactured in previous work, intended to challenge and assess these next-generation technologies and enable comparison between modalities. The ultrasound-compatible phantom generates ring vortices over a range of Reynolds numbers. These vortices were previously visualised using Laser-PIV and noted for their reproducibility at the macro-scale. This work strove to continue the development of this device, by optimising the device, characterising its functionality (both in device and flow) and expanding its modality compatibility. Achieving these objectives would produce a pre-commercial device compatible with both US and MRI, where high confidence is held in its capabilities. Firstly, the phantom vortices were characterised at the micro-scale, with stability of 80% and reproducibility of 10% found for a range of generating conditions. These thresholds established the levels to which this device and its flows can perform. A QA tool was manufactured to ensure these behaviours were met, with device and flow behaviour tracked in real-time to heighten confidence in correct functionality. The device was optimised to ensure efficient and consistent behaviour, through refinement of the device components and flow generating conditions. Phantom vortices were then further characterised in the context of analytical models, with vortices found to behave according to the Kaplanski-Rudi viscous vortex ring model. Updated experimental visualisation was performed on the optimised phantom version, with the vortices found to retain their high stability and reproducibility, and low stroke-ratio rings acting according to Kaplanski-Rudi. This consistent agreement established Kaplanski-Rudi model as a useful tool for analytical ground-truth datasets for flow characterisation. With the ultrasound-compatible phantom suitable for more widespread use, its restriction to US modalities was addressed, and an MRI-compatible version was manufactured. High stability and reproducibility were observed at the macro-scale, and micro-scale analysis revealed Kaplanski-Rudi behaviour despite the significant design change. This proved the consistency of vortex behaviour over a wide range of generating conditions, and its robustness to design changes. This project significantly improved confidence in the ring vortex phantom, through characterising its vortices’ behaviour (experimentally and analytically), demonstrating device functionality in real-time, and retaining its abilities through a significant re-design for MRI application. The ring vortex phantom is now equipped for the final pre-commercial stage, where widespread imaging through clinical and pre-clinical technologies will demonstrate its usefulness and potential

High Frame Rate Ultrasound Velocimetry of Fast Blood Flow Dynamics

In this thesis we develop and validate high frame rate ultrasound sequences for use with echo-particle image velocimetry (in 2D and 3D), with the aim of measuring the high velocity blood flow patterns in the left ventricle and abdominal aorta

Pattern search for the visualization of scalar, vector, and line fields

The main topic of this thesis is pattern search in data sets for the purpose of visual data analysis. By giving a reference pattern, pattern search aims to discover similar occurrences in a data set with invariance to translation, rotation and scaling. To address this problem, we developed algorithms dealing with different types of data: scalar fields, vector fields, and line fields. For scalar fields, we use the SIFT algorithm (Scale-Invariant Feature Transform) to find a sparse sampling of prominent features in the data with invariance to translation, rotation, and scaling. Then, the user can define a pattern as a set of SIFT features by e.g. brushing a region of interest. Finally, we locate and rank matching patterns in the entire data set. Due to the sparsity and accuracy of SIFT features, we achieve fast and memory-saving pattern query in large scale scalar fields. For vector fields, we propose a hashing strategy in scale space to accelerate the convolution-based pattern query. We encode the local flow behavior in scale space using a sequence of hierarchical base descriptors, which are pre-computed and hashed into a number of hash tables. This ensures a fast fetching of similar occurrences in the flow and requires only a constant number of table lookups. For line fields, we present a stream line segmentation algorithm to split long stream lines into globally-consistent segments, which provides similar segmentations for similar flow structures. It gives the benefit of isolating a pattern from long and dense stream lines, so that our patterns can be defined sparsely and have a significant extent, i.e., they are integration-based and not local. This allows for a greater flexibility in defining features of interest. For user-defined patterns of curve segments, our algorithm finds similar ones that are invariant to similarity transformations. Additionally, we present a method for shape recovery from multiple views. This semi-automatic method fits a template mesh to high-resolution normal data. In contrast to existing 3D reconstruction approaches, we accelerate the data acquisition time by omitting the structured light scanning step of obtaining low frequency 3D information.Das Hauptthema dieser Arbeit ist die Mustersuche in Datensätzen zur visuellen Datenanalyse. Durch die Vorgabe eines Referenzmusters versucht die Mustersuche ähnliche Vorkommen in einem Datensatz mit Translations-, Rotations- und Skalierungsinvarianz zu entdecken. In diesem Zusammenhang haben wir Algorithmen entwickelt, die sich mit verschiedenen Arten von Daten befassen: Skalarfelder, Vektorfelder und Linienfelder. Bei Skalarfeldern benutzen wir den SIFT-Algorithmus (Scale-Invariant Feature Transform), um ein spärliches Abtasten von markanten Merkmalen in Daten mit Translations-, Rotations- und Skalierungsinvarianz zu finden. Danach kann der Benutzer ein Muster als Menge von SIFT-Merkmalspunkten definieren, zum Beispiel durch Markieren einer interessierenden Region. Schließlich lokalisieren wir passende Muster im gesamten Datensatz und stufen sie ein. Aufgrund der spärlichen Verteilung und der Genauigkeit von SIFT-Merkmalspunkten erreichen wir eine schnelle und speichersparende Musterabfrage in großen Skalarfeldern. Für Vektorfelder schlagen wir eine Hashing-Strategie zur Beschleunigung der faltungsbasierten Musterabfrage im Skalenraum vor. Wir kodieren das lokale Flussverhalten im Skalenraum durch eine Sequenz von hierarchischen Basisdeskriptoren, welche vorberechnet und als Zahlen in einer Hashtabelle gespeichert sind. Dies stellt eine schnelle Abfrage von ähnlichen Vorkommen im Fluss sicher und benötigt lediglich eine konstante Anzahl von Nachschlageoperationen in der Tabelle. Für Linienfelder präsentieren wir einen Algorithmus zur Segmentierung von Stromlinien, um lange Stromlinen in global konsistente Segmente aufzuteilen. Dies erlaubt eine größere Flexibilität bei der Definition von Mustern. Für vom Benutzer definierte Muster von Kurvensegmenten findet unser Algorithmus ähnliche Kurvensegmente, die unter Ähnlichkeitstransformationen invariant sind. Zusätzlich präsentieren wir eine Methode zur Rekonstruktion von Formen aus mehreren Ansichten. Diese halbautomatische Methode passt ein Template an hochauflösendeNormalendatenan. Im Gegensatz zu existierenden 3D-Rekonstruktionsverfahren beschleunigen wir die Datenaufnahme, indem wir auf die Streifenprojektion verzichten, um niederfrequente 3D Informationen zu gewinnen

New Foundation in the Sciences: Physics without sweeping infinities under the rug

It is widely known among the Frontiers of physics, that “sweeping under the rug” practice has been quite the norm rather than exception. In other words, the leading paradigms have strong tendency to be hailed as the only game in town. For example, renormalization group theory was hailed as cure in order to solve infinity problem in QED theory. For instance, a quote from Richard Feynman goes as follows: “What the three Nobel Prize winners did, in the words of Feynman, was to get rid of the infinities in the calculations. The infinities are still there, but now they can be skirted around . . . We have designed a method for sweeping them under the rug. [1] And Paul Dirac himself also wrote with similar tune: “Hence most physicists are very satisfied with the situation. They say: Quantum electrodynamics is a good theory, and we do not have to worry about it any more. I must say that I am very dissatisfied with the situation, because this so-called good theory does involve neglecting infinities which appear in its equations, neglecting them in an arbitrary way. This is just not sensible mathematics. Sensible mathematics involves neglecting a quantity when it turns out to be small—not neglecting it just because it is infinitely great and you do not want it!”[2] Similarly, dark matter and dark energy were elevated as plausible way to solve the crisis in prevalent Big Bang cosmology. That is why we choose a theme here: New Foundations in the Sciences, in order to emphasize the necessity to introduce a new set of approaches in the Sciences, be it Physics, Cosmology, Consciousness etc