Deconvolution‐based distortion correction of EPI using analytic single‐voxel point‐spread functions

Purpose To develop a postprocessing algorithm that corrects geometric distortions due to spatial variations of the static magnetic field amplitude, B0, and effects from relaxation during signal acquisition in EPI. Theory and Methods An analytic, complex point‐spread function is deduced for k‐space trajectories of EPI variants and applied to corresponding acquisitions in a resolution phantom and in human volunteers at 3 T. With the analytic point‐spread function and experimental maps of B0 (and, optionally, the effective transverse relaxation time, urn:x-wiley:07403194:media:mrm28591:mrm28591-math-0004) as input, a point‐spread function matrix operator is devised for distortion correction by a Thikonov‐regularized deconvolution in image space. The point‐spread function operator provides additional information for an appropriate correction of the signal intensity distribution. A previous image combination algorithm for acquisitions with opposite phase blip polarities is adapted to the proposed method to recover destructively interfering signal contributions. Results Applications of the proposed deconvolution‐based distortion correction (“DecoDisCo”) algorithm demonstrate excellent distortion corrections and superior performance regarding the recovery of an undistorted intensity distribution in comparison to a multifrequency reconstruction. Examples include full and partial Fourier standard EPI scans as well as double‐shot center‐out trajectories. Compared with other distortion‐correction approaches, DecoDisCo permits additional deblurring to obtain sharper images in cases of significant urn:x-wiley:07403194:media:mrm28591:mrm28591-math-0005 effects. Conclusion Robust distortion corrections in EPI acquisitions are feasible with high quality by regularized deconvolution with an analytic point‐spread function. The general algorithm, which is publicly released on GitHub, can be straightforwardly adapted for specific EPI variants or other acquisition schemes

Doctor of Philosophy

dissertationMagnetic resonance imaging (MRI) techniques are widely applied in various disease diagnoses and scientific research projects as noninvasive methods. However, lower signal-to-noise ratio (SNR), B1 inhomogeneity, motion-related artifact, susceptibility artifact, chemical shift artifact and Gibbs ring still play a negative role in image quality improvement. Various techniques and methods were developed to minimize and remove the degradation of image quality originating from artifacts. In the first part of this dissertation, a motion artifact reduction technique based on a novel real time self-gated pulse sequence is presented. Diffusion weighted and diffusion tensor magnetic resonance imaging techniques are generally performed with signal averaging of multiple measurements to improve the signal-to-noise ratio and the accuracy of diffusion measurement. Any discrepancy in images between different averages causes errors that reduce the accuracy of diffusion MRI measurements. The new scheme is capable of detecting a subject's motion and reacquiring motion-corrupted data in real time and helps to improve the accuracy of diffusion MRI measurements. In the second part of this dissertation, a rapid T1 mapping technique (two dimensional singleshot spin echo stimulated echo planar image--2D ss-SESTEPI), which is an EPI-based singleshot imaging technique that simultaneously acquires a spin-EPI (SEPI) and a stimulated-EPI (STEPI) after a single RF excitation, is discussed. The magnitudes of SEPI and STEPI differ by T1 decay for perfect 90o RF pulses and can be used to rapidly measure the T1 relaxation time. However, the spatial variation of B1 amplitude induces uneven splitting of the transverse magnetization for SEPI and STEPI within the imaging FOV. Therefore, correction for B1 inhomogeneity is critical for 2D ss-SESTEPI to be used for T1 measurement. In general, the EPI-based pulse sequence suffers from geometric distortion around the boundary of air-tissue or bone tissue. In the third part of this dissertation, a novel pulse sequence is discussed, which was developed based on three dimensional singleshot diffusion weighted stimulated echo planar imaging (3D ss-DWSTEPI). A parallel imaging technique was combined with 3D ss-DWSTEPI to reduce the image distortion, and the secondary spin echo formed by three RF pulses (900-1800-900) is used to improve the SNR. Image quality is improved

Advances in Concurrent Motion and Field-Inhomogeneity Correction in Functional MRI.

Head motion and static magnetic field (B0) inhomogeneity are two important sources of image intensity variability in functional MRI (fMRI). Ideally, in MRI, any deviation in B0 homogeneity in an object occurs only by design. However, due to imperfections in the main magnet and gradient coils, and, magnetic susceptibility differences in the object, undesired B0 deviations may occur. This causes geometric distortion in Cartesian EPI images. In addition to spatial shifts and rotations of images, head motion during an fMRI experiment may induce time-varying field-inhomogeneity changes in the brain. As a result, correcting for motion and field-inhomogeneity effects independently of each other with a static field map may be insufficient, especially in the presence of large out-of-plane rotations. Our primary concern is the correction of the combined effects of motion and field-inhomogeneity induced geometric distortion in Cartesian EPI fMRI images. We formulate a concurrent field-inhomogeneity with map-slice-to-volume motion correction, and develop a motion-robust dual-echo bipolar gradient echo static field map estimation method. We also propose and evaluate a penalized weighted least squares approach to dynamic field map estimation using the susceptibility voxel convolution method. This technique accounts for field changes due to out-of-plane rotations, and estimates dynamic field maps from a high resolution static field map without requiring accurate image segmentation, or the use of literature susceptibility values. Experiments with simulated data suggest that the technique is promising, and the method will be applied to real data in future work. In a separate clinical fMRI project, which is independent of the above work, we also formulate a current density weighted index to quantify correspondence between electrocortical stimulation and fMRI maps for brain presurgical planning. The proposed index is formulated with the broader goal of defining safe limits for lesion resection, and is characterized extensively with simulated data. The index is also computed for real human datasets.Ph.D.Electrical Engineering: SystemsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/60787/1/tbyeo_1.pd

Motion robust acquisition and reconstruction of quantitative T2* maps in the developing brain

The goal of the research presented in this thesis was to develop methods for quantitative T2* mapping of the developing brain. Brain maturation in the early period of life involves complex structural and physiological changes caused by synaptogenesis, myelination and growth of cells. Molecular structures and biological processes give rise to varying levels of T2* relaxation time, which is an inherent contrast mechanism in magnetic resonance imaging. The knowledge of T2* relaxation times in the brain can thus help with evaluation of pathology by establishing its normative values in the key areas of the brain. T2* relaxation values are a valuable biomarker for myelin microstructure and iron concentration, as well as an important guide towards achievement of optimal fMRI contrast. However, fetal MR imaging is a significant step up from neonatal or adult MR imaging due to the complexity of the acquisition and reconstruction techniques that are required to provide high quality artifact-free images in the presence of maternal respiration and unpredictable fetal motion. The first contribution of this thesis, described in Chapter 4, presents a novel acquisition method for measurement of fetal brain T2* values. At the time of publication, this was the first study of fetal brain T2* values. Single shot multi-echo gradient echo EPI was proposed as a rapid method for measuring fetal T2* values by effectively freezing intra-slice motion. The study concluded that fetal T2* values are higher than those previously reported for pre-term neonates and decline with a consistent trend across gestational age. The data also suggested that longer than usual echo times or direct T2* measurement should be considered when performing fetal fMRI in order to reach optimal BOLD sensitivity. For the second contribution, described in Chapter 5, measurements were extended to a higher field strength of 3T and reported, for the first time, both for fetal and neonatal subjects at this field strength. The technical contribution of this work is a fully automatic segmentation framework that propagates brain tissue labels onto the acquired T2* maps without the need for manual intervention. The third contribution, described in Chapter 6, proposed a new method for performing 3D fetal brain reconstruction where the available data is sparse and is therefore limited in the use of current state of the art techniques for 3D brain reconstruction in the presence of motion. To enable a high resolution reconstruction, a generative adversarial network was trained to perform image to image translation between T2 weighted and T2* weighted data. Translated images could then be served as a prior for slice alignment and super resolution reconstruction of 3D brain image.Open Acces

Quantitative susceptibility mapping and susceptibility-based distortion correction of echo planar images

Thesis (Ph. D. in Medical Engineering)--Harvard-MIT Program in Health Sciences and Technology, 2012.Cataloged from PDF version of thesis.Includes bibliographical references (p. 143-153).The field of medical image analysis continues to expand as magnetic resonance imaging (MRI) technology advances through increases in field strength and the development of new image acquisition and reconstruction methods. The advent of echo planar imaging (EPI) has allowed volumetric data sets to be obtained in a few seconds, making it possible to image dynamic physiological processes in the brain. In order to extract meaningful information from functional and diffusion data, clinicians and neuroscientists typically combine EPI data with high resolution structural images. Image registration is the process of determining the correct correspondence. Registration of EPI and structural images is difficult due to distortions in EPI data. These distortions are caused by magnetic field perturbations that arise from changes in magnetic susceptibility throughout the object of interest. Distortion is typically corrected by acquiring an additional scan called a fieldmap. A fieldmap provides a direct measure of the magnetic perturbations, allowing distortions to be easily computed and corrected. Fieldmaps, however, require additional scan time, may not be reliable in the presence of significant motion or respiration effects, and are often omitted from clinical protocols. In this thesis, we develop a novel method for correcting distortions in EPI data and registering the EPI to structural MRI. A synthetic fieldmap is computed from a tissue/air segmentation of a structural image using a perturbation method and subsequently used to unwarp the EPI data. Shim and other missing parameters are estimated by registration. We obtain results that are similar to those obtained using fieldmnaps, however, neither fieldmaps nor knowledge of shim coefficients is required. In addition, we describe a method for atlas-based segmentation of structural images for calculation of synthetic fieldmaps. CT data sets are used to construct a probabilistic atlas of the head and corresponding MRI is used to train a classifier that segments soft tissue, air, and bone. Synthetic fieldmap results agree well with acquired fieldmaps: 90% of voxel shifts show subvoxel disagreement with those computed from acquired fieldmaps. In addition, synthetic fieldmaps show statistically significant improvement following inclusion of the atlas. In the second part of this thesis, we focus on the inverse problem of reconstructing quantitative magnetic susceptibility maps from acquired fieldmaps. Iron deposits change the susceptibility of tissue, resulting in magnetic perturbations that are detectable with high resolution fieldmaps. Excessive iron deposition in specific regions of the brain is associated with neurodegenerative disorders such as Alzheimer's and Parkinson's disease. In addition, iron is known to accumulate at varying rates throughout the brain in normal aging. Developing a non-invasive method to calculate iron concentration may provide insight into the role of iron in the pathophysiology of neurodegenerative disease. Calculating susceptibility maps from measured fieldmaps is difficult, however, since iron-related field inhomogeneity may be obscured by larger field perturbations, or 'biasfields', arising from adjacent tissue/air boundaries. In addition, the inverse problem is ill-posed, and fieldmap measurements are only valid in limited anatomical regions. In this dissertation, we develop a novel atlas-based susceptibility mapping (ASM) technique that requires only a single fieldmap acquisition and successfully inverts a spatial formulation of the forward field model. We derive an inhomogeneous wave equation that relates the Laplacian of the observed field to the D'Alembertian of susceptibility, and eliminates confounding biasfields. The tissue/air atlas we constructed for susceptibility-based distortion correction is applied to resolve ambiquity in the forward model arising from the ill-posed inversion. We include fourier-based modeling of external susceptibility sources and the associated biasfield in a variational approach, allowing for simultaneous susceptibility estimation and biasfield elimination. Results show qualitative improvement over two methods commonly used to infer underlying susceptibility values and quantitative susceptibility estimates show stronger correlation with postmortem iron concentrations than competing methods.by Clare Poynton.Ph.D.in Medical Engineerin

Image processing methods for human brain connectivity analysis from in-vivo diffusion MRI

In this PhD Thesis proposal, the principles of diffusion MRI (dMRI) in its application to the human brain mapping of connectivity are reviewed. The background section covers the fundamentals of dMRI, with special focus on those related to the distortions caused by susceptibility inhomogeneity across tissues. Also, a deep survey of available correction methodologies for this common artifact of dMRI is presented. Two methodological approaches to improved correction are introduced. Finally, the PhD proposal describes its objectives, the research plan, and the necessary resources

Doctor of Philosophy

dissertationOver the past decade, molecular imaging has emerged as a powerful tool to visualize biological processes of living subjects on the cellular or molecular level. Such techniques greatly improve our understanding of disease and drug activity. Since molecular imaging relies on exoteric imaging agents as reporters to send detectable signals towards the outside, investigation of the imaging agents is of vital importance. However, the quantification of the imaging agents is still one of the challenges facing this work. Magnetic resonance (MR) imaging has been widely used as one of the imaging modalities for molecular imaging. This dissertation focuses on the quantification of the gadolinium based contrast agent (GBCA) and the 19F contained drug and imaging agent used in MR imaging and spectroscopy. MR imaging pulse sequence, hardware and novel imaging agents have been developed to achieve more rapid and accurate quantitative methodologies for determination of imaging agents. In the first part of the dissertation, a rapid T1 and T2 mapping technique ms-DSEPI-T12 is introduced to assess in vivo dynamic T1 profile. Temporal resolution 15 sec has been achieved for the in vivo mice experiments with voxel size of 1.0×1.0×2.0 mm3. Comparing the conventional T1 mapping methods, e.g., inversion recovery, which takes several to tens of minutes, ms-DSEPI-T12 can provide much higher temporal resolution. In the second part, 19F MR spectroscopy has been collected to monitor an ocular corticosteroid, TAP, with total dosage of 9 ?mol using a rabbit model. Intravitreal and subconjunctival injections were used to deliver TAP into the rabbit eyes. The elimination half-lives of TAP in vivo and in postmortem rabbit eyes are 7.8±1.1, 17.2±2.1 Hr using intravitreal injection, and 0.5±0.1, 6.0±1.5 Hr using subconjunctival injection, which are used to investigate the possible ocular elimination pathway of TAP. In the last part, 19F MR imaging using a newly developed 19F MR imaging agent, 19FIT, was done on a 3T clinical system. For the mice experiment, conducted with voxel size 1.5×1.5×3.0 mm3 and 5 min 9 sec imaging time, relatively high SNR (ranges from 10 to 60 in heart, liver and bladder) of the 19F imaging is achieved

Double volumetric navigators for real-time simultaneous shim and motion measurement and correction in Glycogen Chemical Exchange Saturation Transfer (GlycoCEST) MRI

Glycogen is the primary glucose storage mechanism in in living systems and plays a central role in systemic glucose homeostasis. The study of muscle glycogen concentrations in vivo still largely relies on tissue sampling methods via needle biopsy. However, muscle biopsies are invasive and limit the frequency of measurements and the number of sites that can be assessed. Non-invasive methods for quantifying glycogen in vivo are therefore desirable in order to understand the pathophysiology of common diseases with dysregulated glycogen metabolism such as obesity, insulin resistance, and diabetes, as well as glycogen metabolism in sports physiology. Chemical Exchange Saturation Transfer (CEST) MRI has emerged as a non-invasive contrast enhancement technique that enables detection of molecules, like glycogen, whose concentrations are too low to impact the contrast of standard MR imaging. CEST imaging is performed by selectively saturating hydrogen nuclei of the metabolites that are in chemical exchange with those of water molecules and detecting a reduction in MRI signal in the water pool resulting from continuous chemical exchange. However, CEST signal can easily be compromised by artifacts. Since CEST is based on chemical shift, it is very sensitive to field inhomogeneity which may arise from poor initial shimming, subject respiration, heating of shim iron, mechanical vibrations or subject motion. This is a particular problem for molecules that resonate close to water, such as - OH protons in glycogen, where small variations in chemical shift cause misinterpretation of CEST data. The purpose of this thesis was to optimize the CEST MRI sequence for glycogen detection and implement a real-time simultaneous motion and shim correction and measurement method. First, analytical solution of the Bloch-McConnell equations was used to find optimal continuous wave RF pulse parameters for glycogen detection, and results were validated on a phantom with varying glycogen concentrations and in vivo on human calf muscle. Next, the CEST sequence was modified with double volumetric navigators (DvNavs) to measure pose changes and update field of view and zero- and first-order shim parameters. Finally, the impact of B0 field fluctuations on the scan-rescan reproducibility of CEST was evaluated in vivo in 9 volunteers across 10 different scans. Simulation results showed an optimal RF saturation power of 1.5µT and duration of 1s for glycoCEST. These parameters were validated experimentally in vivo and the ability to detect varying glycogen concentrations was demonstrated in a phantom. Phantom data showed that the DvNav-CEST sequence accurately estimates system frequency and linear shim gradient changes due to motion and corrects resulting image distortions. In addition, DvNav-CEST was shown to yield improved CEST quantification in vivo in the presence of motion and motion-induced field inhomogeneity. B0 field fluctuations were found to lower the reproducibility of CEST measures: the mean coefficient of variation (CoV) for repeated scans was 83.70 ± 70.79 % without shim correction. However, the DvNav-CEST sequence was able to measure and correct B0 variations, reducing the CoV to 2.6 ± 1.37 %. The study confirms the possibility of detecting glycogen using CEST MRI at 3 T and shows the potential of the real-time shim and motion navigated CEST sequence for producing repeatable results in vivo by reducing the effect of B0 field fluctuations