A 3D MR-acquisition scheme for nonrigid bulk motion correction in simultaneous PET-MR.

PURPOSE: Positron emission tomography (PET) is a highly sensitive medical imaging technique commonly used to detect and assess tumor lesions. Magnetic resonance imaging (MRI) provides high resolution anatomical images with different contrasts and a range of additional information important for cancer diagnosis. Recently, simultaneous PET-MR systems have been released with the promise to provide complementary information from both modalities in a single examination. Due to long scan times, subject nonrigid bulk motion, i.e., changes of the patient's position on the scanner table leading to nonrigid changes of the patient's anatomy, during data acquisition can negatively impair image quality and tracer uptake quantification. A 3D MR-acquisition scheme is proposed to detect and correct for nonrigid bulk motion in simultaneously acquired PET-MR data. METHODS: A respiratory navigated three dimensional (3D) MR-acquisition with Radial Phase Encoding (RPE) is used to obtain T1- and T2-weighted data with an isotropic resolution of 1.5 mm. Healthy volunteers are asked to move the abdomen two to three times during data acquisition resulting in overall 19 movements at arbitrary time points. The acquisition scheme is used to retrospectively reconstruct dynamic 3D MR images with different temporal resolutions. Nonrigid bulk motion is detected and corrected in this image data. A simultaneous PET acquisition is simulated and the effect of motion correction is assessed on image quality and standardized uptake values (SUV) for lesions with different diameters. RESULTS: Six respiratory gated 3D data sets with T1- and T2-weighted contrast have been obtained in healthy volunteers. All bulk motion shifts have successfully been detected and motion fields describing the transformation between the different motion states could be obtained with an accuracy of 1.71 ± 0.29 mm. The PET simulation showed errors of up to 67% in measured SUV due to bulk motion which could be reduced to less than 10% with the proposed motion compensation approach. CONCLUSIONS: A MR acquisition scheme which yields both high resolution 3D anatomical data and highly accurate nonrigid motion information without an increase in scan time is presented. The proposed method leads to a strong improvement in both MR and PET image quality and ensures an accurate assessment of tracer uptake

Magnetic Resonance Imaging of Short-T2 Tissues with Applications for Quantifying Cortical Bone Water and Myelin

The human body contains a variety of tissue species with short T2 ranging from a few microseconds to hundreds of microseconds. Detection and quantification of these short-T2 species is of considerable clinical and scientific interest. Cortical bone water and myelin are two of the most important tissue constituents. Quantification of cortical bone water concentration allows for indirect estimation of bone pore volume and noninvasive assessment of bone quality. Myelin is essential for the proper functioning of the central nervous system (CNS). Direct assessment of myelin would reveal CNS abnormalities and enhance our understanding of neurological diseases. However, conventional MRI with echo times of several milliseconds or longer is unable to detect these short-lived MR signals. Recent advances in MRI technology and hardware have enabled development of a number of short-T2 imaging techniques, key among which are ultra-short echo time (UTE) imaging, zero echo time (ZTE) imaging, and sweep imaging with Fourier transform (SWIFT). While these pulse sequences are able to detect short-T2 species, they still suffer from signal interference between different T2 tissue constituents, image artifacts and excessive scan time. These are primary technical hurdles for application to whole-body clinical scanners. In this thesis research, new MRI techniques for improving short-T2 tissue imaging have been developed to address these challenges with a focus on direct detection and quantification of cortical bone water and myelin on a clinical MRI scanner. The first focus of this research was to optimize long-T2 suppression in UTE imaging. Saturation and adiabatic RF pulses were designed to achieve maximum long-T2 suppression while maximizing the signal from short-T2 species. The imaging protocols were optimized by Bloch equation simulations and were validated using phantom and in vivo experiments. The results show excellent short-T2 contrast with these optimized pulse sequences. The problem of blurring artifacts resulting from the inhomogeneous excitation profile of the rectangular pulses in ZTE imaging was addressed. The proposed approach involves quadratic phase-modulated RF excitation and iterative solution of an inverse problem formulated from the signal model of ZTE imaging and is shown to effectively remove the image artifacts. Subsequently image acquisition efficiency was improved in order to attain clinically-feasible scan times. To accelerate the acquisition speed in UTE and ZTE imaging, compressed sensing was applied with a hybrid 3D UTE sequence. Further, the pulse sequence and reconstruction procedure were modified to enable anisotropic field-of-view shape conforming to the geometry of the elongated imaged object. These enhanced acquisition techniques were applied to the detection and quantification of cortical bone water. A new biomarker, the suppression ratio (a ratio image derived from two UTE images, one without and the other with long-T2 suppression), was conceived as a surrogate measure of cortical bone porosity. Experimental data suggest the suppression ratio may be a more direct measure of porosity than previously measured total bone water concentration. Lastly, the feasibility of directly detecting and quantifying spatially-resolved myelin concentration with a clinical imager was explored, both theoretically and experimentally. Bloch equation simulations were conducted to investigate the intrinsic image resolution and the fraction of detectable myelin signal under current scanner hardware constraints. The feasibility of quantitative ZTE imaging of myelin extract and lamb spinal cord at 3T was demonstrated. The technological advances achieved in this dissertation research may facilitate translation of short-T2 MRI methods from the laboratory to the clinic

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

Respiratory organ motion in interventional MRI : tracking, guiding and modeling

Respiratory organ motion is one of the major challenges in interventional MRI, particularly in interventions with therapeutic ultrasound in the abdominal region. High-intensity focused ultrasound found an application in interventional MRI for noninvasive treatments of different abnormalities. In order to guide surgical and treatment interventions, organ motion imaging and modeling is commonly required before a treatment start. Accurate tracking of organ motion during various interventional MRI procedures is prerequisite for a successful outcome and safe therapy. In this thesis, an attempt has been made to develop approaches using focused ultrasound which could be used in future clinically for the treatment of abdominal organs, such as the liver and the kidney. Two distinct methods have been presented with its ex vivo and in vivo treatment results. In the first method, an MR-based pencil-beam navigator has been used to track organ motion and provide the motion information for acoustic focal point steering, while in the second approach a hybrid imaging using both ultrasound and magnetic resonance imaging was combined for advanced guiding capabilities. Organ motion modeling and four-dimensional imaging of organ motion is increasingly required before the surgical interventions. However, due to the current safety limitations and hardware restrictions, the MR acquisition of a time-resolved sequence of volumetric images is not possible with high temporal and spatial resolution. A novel multislice acquisition scheme that is based on a two-dimensional navigator, instead of a commonly used pencil-beam navigator, was devised to acquire the data slices and the corresponding navigator simultaneously using a CAIPIRINHA parallel imaging method. The acquisition duration for four-dimensional dataset sampling is reduced compared to the existing approaches, while the image contrast and quality are improved as well. Tracking respiratory organ motion is required in interventional procedures and during MR imaging of moving organs. An MR-based navigator is commonly used, however, it is usually associated with image artifacts, such as signal voids. Spectrally selective navigators can come in handy in cases where the imaging organ is surrounding with an adipose tissue, because it can provide an indirect measure of organ motion. A novel spectrally selective navigator based on a crossed-pair navigator has been developed. Experiments show the advantages of the application of this novel navigator for the volumetric imaging of the liver in vivo, where this navigator was used to gate the gradient-recalled echo sequence

Disambiguating the role of blood flow and global signal with partial information decomposition

Global signal (GS) is an ubiquitous construct in resting state functional magnetic resonance imaging (rs-fMRI), associated to nuisance, but containing by definition most of the neuronal signal. Global signal regression (GSR) effectively removes the impact of physiological noise and other artifacts, but at the same time it alters correlational patterns in unpredicted ways. Performing GSR taking into account the underlying physiology (mainly the blood arrival time) has been proven to be beneficial. From these observations we aimed to: 1) characterize the effect of GSR on network-level functional connectivity in a large dataset; 2) assess the complementary role of global signal and vessels; and 3) use the framework of partial information decomposition to further look into the joint dynamics of the global signal and vessels, and their respective influence on the dynamics of cortical areas. We observe that GSR affects intrinsic connectivity networks in the connectome in a non-uniform way. Furthermore, by estimating the predictive information of blood flow and the global signal using partial information decomposition, we observe that both signals are present in different amounts across intrinsic connectivity networks. Simulations showed that differences in blood arrival time can largely explain this phenomenon, while using hemodynamic and calcium mouse recordings we were able to confirm the presence of vascular effects, as calcium recordings lack hemodynamic information. With these results we confirm network-specific effects of GSR and the importance of taking blood flow into account for improving de-noising methods. Additionally, and beyond the mere issue of data denoising, we quantify the diverse and complementary effect of global and vessel BOLD signals on the dynamics of cortical areas

Quantitative fat and R2* mapping in vivo to measure lipid-rich necrotic core and intraplaque hemorrhage in carotid atherosclerosis

Purpose: The aim of this work was to quantify the extent of lipid-rich necrotic core (LRNC) and intraplaque hemorrhage (IPH) in atherosclerotic plaques. Methods: Patients scheduled for carotid endarterectomy underwent four-point Dixon and T1-weighted magnetic resonance imaging (MRI) at 3 Tesla. Fat and R2* maps were generated from the Dixon sequence at the acquired spatial resolution of 0.60 × 0.60 × 0.70 mm voxel size. MRI and three-dimensional (3D) histology volumes of plaques were registered. The registration matrix was applied to segmentations denoting LRNC and IPH in 3D histology to split plaque volumes in regions with and without LRNC and IPH. Results: Five patients were included. Regarding volumes of LRNC identified by 3D histology, the average fat fraction by MRI was significantly higher inside LRNC than outside: 12.64 ± 0.2737% versus 9.294 ± 0.1762% (mean ± standard error of the mean [SEM]; P < 0.001). The same was true for IPH identified by 3D histology, R2* inside versus outside IPH was: 71.81 ± 1.276 s−1 versus 56.94 ± 0.9095 s−1 (mean ± SEM; P < 0.001). There was a strong correlation between the cumulative fat and the volume of LRNC from 3D histology (R2 = 0.92) as well as between cumulative R2* and IPH (R2 = 0.94). Conclusion: Quantitative mapping of fat and R2* from Dixon MRI reliably quantifies the extent of LRNC and IPH

Field Inhomogeneity Compensation in High Field Magnetic Resonance Imaging (MRI)

This thesis concentrates on the reduction of field (both main field B0 and RF field B1) inhomogeneity in MRI, especially at high B0 field. B0 and B1 field inhomogeneity are major hindrances in high B0 field MRI applications. B1 inhomogeneity will lead to spatially varying signal intensity in the MR images. B0 inhomogeneity produces blurring, distortion and signal loss at tissue interfaces. B0 artifacts are usually termed off-resonance or susceptibility artifacts. None of the existing methods can perfectly correct these inhomogeneity artifacts.This thesis aims at developing three-dimensional (3D) tailored RF (TRF) pulses to mitigate these artifacts. A current limitation in the use of 3D TRF techniques, however, is that pulses are often too long for practical clinical applications. Multiple transmission techniques are proposed to decrease pulse lengths and provide an inherent correction for B1 inhomogeneity. Shorter pulses are also more robust to profile distortions from susceptibility effects.Specifically, slice-selective 3D TRF pulses for multiple (or ¡°parallel¡±) transmitters were designed and validated in uniform phantom and human brain experiments at 3 Tesla. A pseudo-transmit sensitivity encoding (¡°transmit SENSE¡±) method was introduced using a body coil transmitter and multiple receivers to mimic the real parallel transmitter experiment. The kz-direction was controlled by fast switching of gradients in a fashion similar to Echo planar imaging (EPI). The transverse plane (kx-ky) was sampled sparsely with hexagonal trajectories, and accelerated with the transmit SENSE method. The transmit SENSE 3D TRF pulses reduced the B1 inhomogeneity compared to standard SINC pulses in human brain scans. The undersampled transmit SENSE pulses were only 4.3ms long and could excite a 5mm thick slice, which is very promising for clinical applications. Furthermore, these pulses are shown by numerical simulation to have promise in correcting through-plane susceptibility artifacts

Development of Methodologies for Diffusion-weighted Magnetic Resonance Imaging at High Field Strength

Diffusion-weighted imaging of small animals at high field strengths is a challenging prospect due to its extreme sensitivity to motion. Periodically rotated overlapping parallel lines with enhanced reconstruction (PROPELLER) was introduced at 9.4T as an imaging method that is robust to motion and distortion. Proton density (PD)-weighted and T2-weighted PROPELLER data were generally superior to that acquired with single-shot, Cartesian and echo planar imaging-based methods in terms of signal-to-noise ratio (SNR), contrast-to-noise ratio and resistance to artifacts. Simulations and experiments revealed that PROPELLER image quality was dependent on the field strength and echo times specified. In particular, PD-weighted imaging at high field led to artifacts that reduced image contrast. In PROPELLER, data are acquired in progressively rotated blades in k-space and combined on a Cartesian grid. PROPELLER with echo truncation at low spatial frequencies (PETALS) was conceived as a postprocessing method that improved contrast by reducing the overlap of k-space data from different blades with different echo times. Where the addition of diffusion weighting gradients typically leads to catastrophic motion artifacts in multi-shot sequences, diffusion-weighted PROPELLER enabled the acquisition of high quality, motion-robust data. Applications in the healthy mouse brain and abdomen at 9.4T and in stroke patients at 3T are presented. PROPELLER increases the minimum scan time by approximately 50%. Consequently, methods were explored to reduce the acquisition time. Two k-space undersampling regimes were investigated by examining image fidelity as a function of degree of undersampling. Undersampling by acquiring fewer k-space blades was shown to be more robust to motion and artifacts than undersampling by expanding the distance between successive phase encoding steps. To improve the consistency of undersampled data, the non-uniform fast Fourier transform was employed. It was found that acceleration factors of up to two could be used with minimal visual impact on image fidelity. To reduce the number of scans required for isotropic diffusion weighting, the use of rotating diffusion gradients was investigated, exploiting the rotational symmetry of the PROPELLER acquisition. Fixing the diffusion weighting direction to the individual rotating blades yielded geometry and anisotropy-dependent diffusion measurements. However, alternating the orientations of diffusion weighting with successive blades led to more accurate measurements of the apparent diffusion coefficient while halving the overall acquisition time. Optimized strategies are proposed for the use of PROPELLER in rapid high resolution imaging at high field strength