A Practical Study of Longitudinal Reference Based Compressed Sensing for MRI

Compressed sensing (CS) is a new signal acquisition paradigm that enables the reconstruction of signals and images from a low number of samples. A particularly exciting application of CS is Magnetic Resonance Imaging (MRI), where CS significantly speeds up scan time by requiring far fewer measurements than standard MRI techniques. Such a reduction in sampling time leads to less power consumption, less need for patient sedation, and more accurate images. This accuracy increase is especially pronounced in pediatric MRI where patients have trouble being still for long scan periods. Although such gains are already significant, even further improvements can be made by utilizing past MRI scans of the same patient. Many patients require repeated scans over a period of time in order to track illnesses and the prior scans can be used as references for the current image. This allows samples to be taken adaptively, based on both the prior scan and the current measurements. Work by Weizman [20] has shown that so-called reference based adaptive-weighted temporal Compressed Sensing MRI (LACS-MRI) requires far fewer samples than standard Compressed Sensing (CS) to achieve the same reconstruction signal-to-noise ratio (RSNR). The method uses a mixture of reference-based and adaptive-sampling. In this work, we test this methodology by using various adaptive sensing schemes, reconstruction methods, and image types. We create a thorough catalog of reconstruction behavior and success rates that is interesting from a mathematical point of view and is useful for practitioners. We also solve a grayscale compensation toy problem that supports the insensitivity of LACS-MRI to changes in MRI acquisition parameters and thus showcases the reliability of LACS-MRI in possible clinical situations

A Practical Study of Longitudinal Reference Based Compressed Sensing for MRI

Compressed sensing (CS) is a new signal acquisition paradigm that enables the reconstruction of signals and images from a low number of samples. A particularly exciting application of CS is Magnetic Resonance Imaging (MRI), where CS significantly speeds up scan time by requiring far fewer measurements than standard MRI techniques. Such a reduction in sampling time leads to less power consumption, less need for patient sedation, and more accurate images. This accuracy increase is especially pronounced in pediatric MRI where patients have trouble being still for long scan periods. Although such gains are already significant, even further improvements can be made by utilizing past MRI scans of the same patient. Many patients require repeated scans over a period of time in order to track illnesses and the prior scans can be used as references for the current image. This allows samples to be taken adaptively, based on both the prior scan and the current measurements. Work by Weizman has shown that so-called reference based adaptive-weighted temporal Compressed Sensing MRI (LACS-MRI) requires far fewer samples than standard Compressed Sensing (CS) to achieve the same reconstruction signal-to-noise ratio (RSNR). The method uses a mixture of reference-based and adaptive-sampling. In this work, we test this methodology by using various adaptive sensing schemes, reconstruction methods, and image types. We create a thorough catalog of reconstruction behavior and success rates that is interesting from a mathematical point of view and is useful for practitioners. We also solve a grayscale compensation toy problem that supports the insensitivity of LACS-MRI to changes in MRI acquisition parameters and thus showcases the reliability of LACS-MRI in possible clinical situations

Under-Sampled Reconstruction Techniques for Accelerated Magnetic Resonance Imaging

Due to physical and biological constraints and requirements on the minimum resolution and SNR, the acquisition time is relatively long in magnetic resonance imaging (MRI). Consequently, a limited number of pulse sequences can be run in a clinical MRI session because of constraints on the total acquisition time due to patient comfort and cost considerations. Therefore, it is strongly desired to reduce the acquisition time without compromising the reconstruction quality. This thesis concerns under-sampled reconstruction techniques for acceleration of MRI acquisitions, i.e., parallel imaging and compressed sensing. While compressed sensing MRI reconstructions are commonly regularized by penalizing the decimated wavelet transform coefficients, it is shown in this thesis that the visual artifacts, associated with the lack of translation-invariance of the wavelet basis in the decimated form, can be avoided by penalizing the undecimated wavelet transform coefficients, i.e., the stationary wavelet transform (SWT). An iterative SWT thresholding algorithm for combined SWT-regularized compressed sensing and parallel imaging reconstruction is presented. Additionally, it is shown that in MRI applications involving multiple sequential acquisitions, e.g., quantitative T1/T2 mapping, the correlation between the successive acquisitions can be incorporated as an additional constraint for joint under-sampled reconstruction, resulting in improved reconstruction performance. While quantitative measures of quality, e.g., reconstruction error with respect to the fully-sampled reference, are commonly used for performance evaluation and comparison of under-sampled reconstructions, this thesis shows that such quantitative measures do not necessarily correlate with the subjective quality of reconstruction as perceived by radiologists and other expert end users. Therefore, unless accompanied by subjective evaluations, quantitative quality measurements/comparisons will be of limited clinical impact. The results of experiments aimed at subjective evaluation/comparison of different under-sampled reconstructions for specific clinical neuroimaging MRI applications are presented in this thesis. One motivation behind the current work was to reduce the acquisition time for relaxation mapping techniques DESPOT1 and DESPOT2. This work also includes a modification to the Driven Equilibrium Single Pulse Observation of T1 with high-speed incorporation of RF field inhomogeneities (DESPOT1-HIFI), resulting in more accurate estimation of T1 values at high strength (3T and higher) magnetic fields

Doctor of Philosophy

dissertationDiffusion tensor MRI (DT-MRI or DTI) has been proven useful for characterizing biological tissue microstructure, with the majority of DTI studies having been performed previously in the brain. Other studies have shown that changes in DTI parameters are detectable in the presence of cardiac pathology, recovery, and development, and provide insight into the microstructural mechanisms of these processes. However, the technical challenges of implementing cardiac DTI in vivo, including prohibitive scan times inherent to DTI and measuring small-scale diffusion in the beating heart, have limited its widespread usage. This research aims to address these technical challenges by: (1) formulating a model-based reconstruction algorithm to accurately estimate DTI parameters directly from fewer MRI measurements and (2) designing novel diffusion encoding MRI pulse sequences that compensate for the higher-order motion of the beating heart. The model-based reconstruction method was tested on undersampled DTI data and its performance was compared against other state-of-the-art reconstruction algorithms. Model-based reconstruction was shown to produce DTI parameter maps with less blurring and noise and to estimate global DTI parameters more accurately than alternative methods. Through numerical simulations and experimental demonstrations in live rats, higher-order motion compensated diffusion-encoding was shown to successfully eliminate signal loss due to motion, which in turn produced data of sufficient quality to accurately estimate DTI parameters, such as fiber helix angle. Ultimately, the model-based reconstruction and higher-order motion compensation methods were combined to characterize changes in the cardiac microstructure in a rat model with inducible arterial hypertension in order to demonstrate the ability of cardiac DTI to detect pathological changes in living myocardium

Estimation of Fiber Orientations Using Neighborhood Information

Data from diffusion magnetic resonance imaging (dMRI) can be used to reconstruct fiber tracts, for example, in muscle and white matter. Estimation of fiber orientations (FOs) is a crucial step in the reconstruction process and these estimates can be corrupted by noise. In this paper, a new method called Fiber Orientation Reconstruction using Neighborhood Information (FORNI) is described and shown to reduce the effects of noise and improve FO estimation performance by incorporating spatial consistency. FORNI uses a fixed tensor basis to model the diffusion weighted signals, which has the advantage of providing an explicit relationship between the basis vectors and the FOs. FO spatial coherence is encouraged using weighted l1-norm regularization terms, which contain the interaction of directional information between neighbor voxels. Data fidelity is encouraged using a squared error between the observed and reconstructed diffusion weighted signals. After appropriate weighting of these competing objectives, the resulting objective function is minimized using a block coordinate descent algorithm, and a straightforward parallelization strategy is used to speed up processing. Experiments were performed on a digital crossing phantom, ex vivo tongue dMRI data, and in vivo brain dMRI data for both qualitative and quantitative evaluation. The results demonstrate that FORNI improves the quality of FO estimation over other state of the art algorithms.Comment: Journal paper accepted in Medical Image Analysis. 35 pages and 16 figure

Advanced H-1 Lung Magnetic Resonance Imaging

Magnetic resonance imaging (MRI) is one of the widely used medical imaging modality, since it can provide both structural and functional assessment in a single imaging session. However, two major challenges should be considered by using MRI for lung imaging. The first challenge is the intrinsic low SNR of H-1 lung MRI due to the low proton density as well as the fast decay of the lung parenchyma signal. And the second challenge is subject motion. To achieve high resolution structural image, MRI requires a long scan time, usually a few minutes or even longer, which make MRI sensitive to subject motion. To address the first challenge, ultra-short echo time (UTE) MRI sequence is used to capture the lung parenchyma signal before decay. As for subject motion, two major strategies are widely used. One strategy is fast breath-holding scan, the subjects are asked to hold their breaths for a short duration, and the fast 3D MR sequence would be used to acquire data within that duration. This dissertation proposes a new acquisition scheme based on the standard UTE sequence, which largely increases the encoding efficiency and improves the breath-holding scan images. The other is free breathing scan with motion correction. The subjects are allowed to breathe during the MR acquisition. After the acquisition, the motion corrupted data would go through the motion correction step to reconstruct the motion free images. In this dissertation, two novel motion corrected reconstruction strategies are proposed to incorporate the motion modeling and compensation into the reconstruction to get high SNR motion corrected 3D and 4D images. When translating the developed techniques to the clinical studies, specifically for pediatric and neonatal studies, more practical problems need to be considered, such as smaller but finer anatomy to image, the different respiratory patterns of the young subjects etc. This dissertation proposes a 5-minute free breathing UTE MRI strategy to achieve a 3D high resolution motion free lung image for pediatric and neonatal studies

Correcting for T1 bias in Magnetization Transfer Saturation (MTsat) Maps Using Sparse-MP2RAGE

Purpose: Magnetization transfer saturation (MTsat) mapping is commonly used to examine the macromolecular content of brain tissue. This study compared variable flip angle (VFA) T1 mapping against compressed sensing (cs)MP2RAGE T1 mapping for accelerating MTsat imaging. Methods: VFA, MP2RAGE and csMP2RAGE were compared against inversion recovery (IR) T1 in a phantom at 3 Tesla. The same 1 mm VFA, MP2RAGE and csMP2RAGE protocols were acquired in four healthy subjects to compare the resulting T1 and MTsat. Bloch-McConnell simulations were used to investigate differences between the phantom and in vivo T1 results. Finally, ten healthy controls were imaged twice with the csMP2RAGE MTsat protocol to quantify repeatability. Results: The MP2RAGE and csMP2RAGE protocols were 13.7% and 32.4% faster than the VFA protocol, respectively. All approaches provided accurate T1 values (<5% difference) in the phantom, but the accuracy of the T1 times was more impacted by differences in T2 for VFA than for MP2RAGE. In vivo, VFA generated longer T1 times than MP2RAGE and csMP2RAGE. Simulations suggest that the bias in the T1 values between VFA and IR-based approaches (MP2RAGE and IR) could be explained by the MT-effects from the inversion pulse. In the test-retest experiment, we found that the csMP2RAGE has a minimum detectable change of 3% for T1 mapping and 7.9% for MTsat imaging. Conclusions: We demonstrated that csMP2RAGE can be used in place of VFA T1 mapping in an MTsat protocol. Furthermore, a shorter scan time and high repeatability can be achieved using the csMP2RAGE sequence.Comment: 23 pages, 7 figures, 2 table