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  1. Abstract Purpose

    The constrained one‐step spectral CT image reconstruction (cOSSCIR) algorithm with a nonconvex alternating direction method of multipliers optimizer is proposed for addressing computed tomography (CT) metal artifacts caused by beam hardening, noise, and photon starvation. The quantitative performance of cOSSCIR is investigated through a series of photon‐counting CT simulations.

    Methods

    cOSSCIR directly estimates basis material maps from photon‐counting data using a physics‐based forward model that accounts for beam hardening. The cOSSCIR optimization framework places constraints on the basis maps, which we hypothesize will stabilize the decomposition and reduce streaks caused by noise and photon starvation. Another advantage of cOSSCIR is that the spectral data need not be registered, so that a ray can be used even if some energy window measurements are unavailable. Photon‐counting CT acquisitions of a virtual pelvic phantom with low‐contrast soft tissue texture and bilateral hip prostheses were simulated. Bone and water basis maps were estimated using the cOSSCIR algorithm and combined to form a virtual monoenergetic image for the evaluation of metal artifacts. The cOSSCIR images were compared to a “two‐step” decomposition approach that first estimated basis sinograms using a maximum likelihood algorithm and then reconstructed basis maps using an iterative total variation constrained least‐squares optimization (MLE+TV). Images were also compared to a nonspectral TV reconstruction of the total number of counts detected for each ray with and without normalized metal artifact reduction (NMAR) applied. The simulated metal density was increased to investigate the effects of increasing photon starvation. The quantitative error and standard deviation in regions of the phantom were compared across the investigated algorithms. The ability of cOSSCIR to reproduce the soft‐tissue texture, while reducing metal artifacts, was quantitatively evaluated.

    Results

    Noiseless simulations demonstrated the convergence of the cOSSCIR and MLE+TV algorithms to the correct basis maps in the presence of beam‐hardening effects. When noise was simulated, cOSSCIR demonstrated a quantitative error of −1 HU, compared to 2 HU error for the MLE+TV algorithm and −154 HU error for the nonspectral TV+NMAR algorithm. For the cOSSCIR algorithm, the standard deviation in the central iodine region of interest was 20 HU, compared to 299 HU for the MLE+TV algorithm, 41 HU for the MLE+TV+Mask algorithm that excluded rays through metal, and 55 HU for the nonspectral TV+NMAR algorithm. Increasing levels of photon starvation did not impact the bias or standard deviation of the cOSSCIR images. cOSSCIR was able to reproduce the soft‐tissue texture when an appropriate regularization constraint value was selected.

    Conclusions

    By directly inverting photon‐counting CT data into basis maps using an accurate physics‐based forward model and a constrained optimization algorithm, cOSSCIR avoids metal artifacts due to beam hardening, noise, and photon starvation. The cOSSCIR algorithm demonstrated improved stability and accuracy compared to a two‐step method of decomposition followed by reconstruction.

     
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  2. Abstract

    Iterative thresholding algorithms seek to optimize a differentiable objective function over a sparsity or rank constraint by alternating between gradient steps that reduce the objective and thresholding steps that enforce the constraint. This work examines the choice of the thresholding operator and asks whether it is possible to achieve stronger guarantees than what is possible with hard thresholding. We develop the notion of relative concavity of a thresholding operator, a quantity that characterizes the worst-case convergence performance of any thresholding operator on the target optimization problem. Surprisingly, we find that commonly used thresholding operators, such as hard thresholding and soft thresholding, are suboptimal in terms of worst-case convergence guarantees. Instead, a general class of thresholding operators, lying between hard thresholding and soft thresholding, is shown to be optimal with the strongest possible convergence guarantee among all thresholding operators. Examples of this general class includes $\ell _q$ thresholding with appropriate choices of $q$ and a newly defined reciprocal thresholding operator. We also investigate the implications of the improved optimization guarantee in the statistical setting of sparse linear regression and show that this new class of thresholding operators attain the optimal rate for computationally efficient estimators, matching the Lasso.

     
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  3. Free, publicly-accessible full text available April 1, 2024
  4. Chen, Xi (Ed.)
    In patients with dense breasts or at high risk of breast cancer, dynamic contrast enhanced MRI (DCE-MRI) is a highly sensitive diagnostic tool. However, its specificity is highly variable and sometimes low; quantitative measurements of contrast uptake parameters may improve specificity and mitigate this issue. To improve diagnostic accuracy, data need to be captured at high spatial and temporal resolution. While many methods exist to accelerate MRI temporal resolution, not all are optimized to capture breast DCE-MRI dynamics. We propose a novel, flexible, and powerful framework for the reconstruction of highly-undersampled DCE-MRI data: enhancement-constrained acceleration (ECA). Enhancement-constrained acceleration uses an assumption of smooth enhancement at small time-scale to estimate points of smooth enhancement curves in small time intervals at each voxel. This method is tested in silico with physiologically realistic virtual phantoms, simulating state-of-the-art ultrafast acquisitions at 3.5s temporal resolution reconstructed at 0.25s temporal resolution (demo code available here). Virtual phantoms were developed from real patient data and parametrized in continuous time with arterial input function (AIF) models and lesion enhancement functions. Enhancement-constrained acceleration was compared to standard ultrafast reconstruction in estimating the bolus arrival time and initial slope of enhancement from reconstructed images. We found that the ECA method reconstructed images at 0.25s temporal resolution with no significant loss in image fidelity, a 4x reduction in the error of bolus arrival time estimation in lesions ( p < 0.01) and 11x error reduction in blood vessels ( p < 0.01). Our results suggest that ECA is a powerful and versatile tool for breast DCE-MRI. 
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  5. Spatial population genetic data often exhibits ‘isolation-by-distance,’ where genetic similarity tends to decrease as individuals become more geographically distant. The rate at which genetic similarity decays with distance is often spatially heterogeneous due to variable population processes like genetic drift, gene flow, and natural selection. Petkova et al., 2016 developed a statistical method called Estimating Effective Migration Surfaces (EEMS) for visualizing spatially heterogeneous isolation-by-distance on a geographic map. While EEMS is a powerful tool for depicting spatial population structure, it can suffer from slow runtimes. Here, we develop a related method called Fast Estimation of Effective Migration Surfaces (FEEMS). FEEMS uses a Gaussian Markov Random Field model in a penalized likelihood framework that allows for efficient optimization and output of effective migration surfaces. Further, the efficient optimization facilitates the inference of migration parameters per edge in the graph, rather than per node (as in EEMS). With simulations, we show conditions under which FEEMS can accurately recover effective migration surfaces with complex gene-flow histories, including those with anisotropy. We apply FEEMS to population genetic data from North American gray wolves and show it performs favorably in comparison to EEMS, with solutions obtained orders of magnitude faster. Overall, FEEMS expands the ability of users to quickly visualize and interpret spatial structure in their data. 
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