Blind Retrospective Motion Correction of MR Images

Die Bewegung des Patienten während einer MRI Untersuchung kann die Bildqualität stark verringern. Eine Verschiebung des abzubildenden Objektes von nur ein Paar Millimetern ist genug um Bewegungsartefakte zu erzeugen und der Scan unbrauchbar für die medizinische Diagnostik zu machen. Obwohl in den letzten 20 Jahren mehrere Verfahren entwickelt wurden, ist die Bewegungskorrektur immer noch ein ungelöstes Problem. Wir schlagen einen neuen retrospektiven Bewegungskorrekturalgorithmus vor, mit dem man die Qualität von 3D MR Bildern verbessern kann. Mit diesem Verfahren ist es möglich sowohl starre als auch nicht starre Körperbewegungen zu korrigieren. Der wichtigste Aspekt unserer Algorithmen ist, dass keine Informationen über die Bewegungstrajektorie, z. B. von Kameras, nötig sind um die Bewegungskorrektur durchzuführen. Unsere Verfahren verwenden die RAW-Dateien von normalen MRT-Sequenzen und brauchen keinerlei Anderungen im Scanablauf. Wir benutzen Grafikprozessoren um die Bewegungskorrektur zu beschleunigen – im Fall von starren Körperbewegungen sind nur wenige Sekunden erforderlich, bei nicht starrer Körperbewegung nur einige Minuten Unser Bewegungskorrekturalgorithmus für starre Körper basiert auf der Minimierung einer Kostenfunktion, die die objektive Qualit ̈at des korrigierten Bildes abschätzt. Die Hauptidee ist, durch Optimierung eine Bewegungstrajektorie zu finden, die den kleinsten Betrag der Kostenfunktion liefert. Wir verwenden die Entropie der Bildgradienten als Bildqualitätsfunktion. Um nicht starre Körperbewegungen zu korrigieren, erweitern wir unser mathematisches Modell von Bewegungseffekten. Wir approximieren nicht starre Körperbewegungen als mehrere lokale starre Körperbewegungen. Um solche Bewegungen zu korrigieren, entwickeln wir ein neues annealing-basiert Optimierungsverfahren. Während der Optimierung wechseln wir zwei Schritte ab - die Kostenfunktionsminimierung durch Bild- und Bewegungsparameter. Wir haben mehrere Simulationen sowie in vivo Versuche am Menschen durchgeführt – beide lieferten wesentliche Bildqualitätsverbesserungen

Parameterisation of M.R. system performance : towards optimised measures of image quality

This thesis proposes optimal measures for the inter-system comparison of signal properties when assessing the imaging performance of Magnetic Resonance Imaging (MRI) scanners. MRI has become a popular clinical imaging modality and there are many manufacturers producing systems of various quality. It is essential, therefore, that the performance of each MRI system can be measured and compared. Five criteria have been identified as being of prime importance, namely, the signal-to-noise ratio (SNR), signal non-uniformity, resolution, system induced ghost artefacts and patient induced ghost artefacts. The research concentrated directly on the derivation of performance parameters from test object images. For each criterion a specific algorithm has been developed to obtain optimal parameters. For SNR, a method of evaluation has been derived that utilises the Wiener spectrum to distinguish between random and non-random noise in the MR image. The assessment of signal non-uniformity has been improved by applying statistical parameters. The Modulation Transfer Function has been used in the evaluation and comparison of resolution of MRI systems. Crosscorrelation techniques have enabled the complete automatic location and analysis of ghost artefacts in MR test object images. An autocorrelation technique has been created to compare the degree of respiratory motion artefact present in an MR image. All the techniques, wherever possible, have been optimised for speed and automated to eliminate operator dependency. The strength of this thesis lies in the fact that the data used is not simulated, it is actual data gathered with the full support of each manufacturer in the country of origin. This enables truly applicable comparison parameters to be derived. This is a prominent deficiency for workers who mathematically create images or who work with only one system. The success of the five parameterisations is demonstrated by performing an inter-system comparison of ten commercially available scanners.Open Acces

Functional anatomy of a visuomotor transformation in the optic tectum of zebrafish

Animals detect sensory cues in their environment and process this information in order to carry out adaptive behavioral responses. To generate target - directed movements, the brain transforms structured sensory inputs into coordinated motor com mands. Some of these behaviors, such as escaping from a predator or approaching a prey, need to be fast and reproducible. The optic tectum of vertebrates (named "superior colliculus" in mammals) is the main target of visual information and is known to play a pivotal role in these kinds of visuomotor transformation. In my dissertation, I investigated the neuronal circuits that map visual cues to motor commands, with a focus on the axonal projections that connect the tectum to premotor areas of the tegmentum and hindbrain. To address these questions, I developed and combined several techniques to link functional information and anatomy to behavior. The animal I chose for my studies is the zebrafish larva, which is amenable to transgenesis, optical imaging appr oaches, optogenetics and behavioral recordings in virtual reality arenas. In a first study, I designed, generated and characterized BAC transgenic lines, which allow gene - specific labelling of neurons and intersectional genetics using Cre - mediated recombination. Importantly, I generated a pan - neuronal line that facilitates brain registrations in order to compare different expression patterns (Förster et al., 2017 b ). In a second project , I contributed to the development of an approach that combines t wo - photon holographic optogenetic stimulation with whole brain calcium imaging, behavior tracking and morphological reconstruction. In this study, I designed the protocol to reveal the anatomical identity of optogenetically targeted individual neurons (dal Maschio et al., 2017). In a third project, I took advantage of some of these methods, including whole - brain calcium imaging, optogenetics and brain registrations, to elucidate how the tectum is wired to make behavioral decisions and to steer behavior dire ctionality. The results culminated in a third manuscript (Helmbrecht et al., submitted), which reported four main findings. First, I optogenetically demonstrated a retinotopic organization of the tectal motor map in zebrafish larvae. Second, I generated a tectal "projectome" with cellular resolution, by reconstructing and registering stochastically labeled tectal projection neurons. Third, by employing this anatomical atlas to interpret functional imaging data, I asked whether visual information leaves the tectum via distinct projection neurons. This revealed that two distinct uncrossed tectobulbar pathways (ipsilateral tectobulbar tract, iTB) are involved in either avoidance (medial iTB, iTB - M) or approach (lateral iTB, iTB - L) behavior. Finally, I showed th at the location of a prey - like object, and therefore the direction of orientation swims towards prey, is functionally encoded in iTB - L projection neurons. In summary, I demonstrated in this thesis how refined genetic and optical methods can be used to stu dy neuronal circuits with cellular and subcellular resolution. Importantly, apart from the biological findings on the visuomotor transformation, these newly developed tools can be broadly employed to link brain anatomy to circuit activity and behavior

Topics in Steady-state MRI Sequences and RF Pulse Optimization.

Small-tip fast recovery (STFR) is a recently proposed rapid steady-state magnetic resonance imaging (MRI) sequence that has the potential to be an alternative to the popular balanced steady-state free precession (bSSFP) imaging sequence, since they have similar signal level and tissue contrast, but STFR has reduced banding artifacts. In this dissertation, an analytic equation of the steady-state signal for the unspoiled version of STFR is first derived. It is shown that unspoiled-STFR is less sensitive to the inaccuracy in excitation than the previous proposed spoiled-STFR. By combining unspoiled-STFR with jointly designed tip-down and tip-up pulses, a 3D STFR acquisition over 3-4 cm thick 3D ROI with single coil and short RF pulses (1.7 ms) is demonstrated. Then, it is demonstrated that STFR can reliably detect functional MRI signal and the contrast is driven mainly from intra-voxel dephasing, not diffusion, using Monte Carlo simulation, human experiments and test-retest reliability. Following that another version of STFR using a spectral pre-winding pulse instead of the spatially tailored pulse is investigated, leading to less T2* weighting, easier implementation. Multidimensional selective RF pulse is a key part for STFR and many other MRI applications. Two novel RF pulse optimization methods are proposed. First, a minimax formulation that directly controls the maximum excitation error, and an effective optimization algorithm using variable splitting and alternating direction method of multipliers (ADMM). The proposed method reduced the maximum excitation by more than half in all the testing cases. Second, a method that jointly optimizes the excitation k-space trajectory and RF pulse is proposed. The k-space trajectory is parametrized using 2nd-order B-splines, and an interior point algorithm is used to explicitly solve the constrained optimization. An effective initialization method is also suggested. The joint design reduced the NRMSE by more than 30 percent compared to existing methods in inner volume excitation and pre-phasing problem. Using the proposed joint design, rapid inner volume STFR imaging with a 4 ms excitation pulse with single transmit coil is demonstrated. Finally, a regularized Bloch-Siegert B1 map reconstruction method is presented that significantly reduces the noise in estimated B1 maps.PhDElectrical Engineering: SystemsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/111514/1/sunhao_1.pd

Entropy in Image Analysis II

Image analysis is a fundamental task for any application where extracting information from images is required. The analysis requires highly sophisticated numerical and analytical methods, particularly for those applications in medicine, security, and other fields where the results of the processing consist of data of vital importance. This fact is evident from all the articles composing the Special Issue "Entropy in Image Analysis II", in which the authors used widely tested methods to verify their results. In the process of reading the present volume, the reader will appreciate the richness of their methods and applications, in particular for medical imaging and image security, and a remarkable cross-fertilization among the proposed research areas

Microscopy Conference 2021 (MC 2021) - Proceedings

Das Dokument enthält die Kurzfassungen der Beiträge aller Teilnehmer an der Mikroskopiekonferenz "MC 2021"

Microscopy Conference 2017 (MC 2017) - Proceedings

Das Dokument enthält die Kurzfassungen der Beiträge aller Teilnehmer an der Mikroskopiekonferenz "MC 2017", die vom 21. bis 25.08.2017, in Lausanne stattfand

Microscopy Conference 2017 (MC 2017) - Proceedings

Das Dokument enthält die Kurzfassungen der Beiträge aller Teilnehmer an der Mikroskopiekonferenz "MC 2017", die vom 21. bis 25.08.2017, in Lausanne stattfand

1996 Laboratory directed research and development annual report

This report summarizes progress from the Laboratory Directed Research and Development (LDRD) program during fiscal year 1996. In addition to a programmatic and financial overview, the report includes progress reports from 259 individual R&D projects in seventeen categories. The general areas of research include: engineered processes and materials; computational and information sciences; microelectronics and photonics; engineering sciences; pulsed power; advanced manufacturing technologies; biomedical engineering; energy and environmental science and technology; advanced information technologies; counterproliferation; advanced transportation; national security technology; electronics technologies; idea exploration and exploitation; production; and science at the interfaces - engineering with atoms