Browsing by Subject "reconstruction"
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Item Open Access Construction of the Jacobian matrix for fluorescence diffuse optical tomography using a perturbation Monte Carlo method.(Proc SPIE Int Soc Opt Eng, 2012-02-13) Zhang, XiaofengImage formation in fluorescence diffuse optical tomography is critically dependent on construction of the Jacobian matrix. For clinical and preclinical applications, because of the highly heterogeneous characteristics of the medium, Monte Carlo methods are frequently adopted to construct the Jacobian. Conventional adjoint Monte Carlo method typically compute the Jacobian by multiplying the photon density fields radiated from the source at the excitation wavelength and from the detector at the emission wavelength. Nonetheless, this approach assumes that the source and the detector in Green's function are reciprocal, which is invalid in general. This assumption is particularly questionable in small animal imaging, where the mean free path length of photons is typically only one order of magnitude smaller than the representative dimension of the medium. We propose a new method that does not rely on the reciprocity of the source and the detector by tracing photon propagation entirely from the source to the detector. This method relies on the perturbation Monte Carlo theory to account for the differences in optical properties of the medium at the excitation and the emission wavelengths. Compared to the adjoint methods, the proposed method is more valid in reflecting the physical process of photon transport in diffusive media and is more efficient in constructing the Jacobian matrix for densely sampled configurations.Item Open Access Diabetic limb salvage procedure with bone allograft and free flap transfer: a case report.(Diabetic foot & ankle, 2017-01) Godoy-Santos, Alexandre L; Amodio, Daniel T; Pires, André; Lima, Ana LM; Wei, Teng H; de Cesar-Netto, Cesar; Armstrong, David GThe aim of this case report was to describe a successful diabetic limb salvage procedure in the treatment of an infected diabetic foot ulcer through a multidisciplinary team approach and complex surgical reconstruction involving a femoral head bone allograft and musculocutaneous latissimus dorsi free flap. The decision to proceed with aggressive staged efforts at diabetic limb salvage should be made only after careful consultation with the patient, his or her family, and the rest of the multidisciplinary healthcare team.Item Open Access How war-related deprivation affects political participation: Evidence from education loss in Liberia(Journal of Peace Research, 2022-05-01) Liu, SXHow does civil war affect citizen engagement with democracy? Civilians who live through warfare face numerous disruptions to everyday life that can have permanent effects on political engagement even after peace is achieved. This article analyzes the role of depressed living standards resulting from education loss during the Liberia Civil War as a case study of war-related deprivation. I argue that the negative effects of war on education and economic outcomes clash with the expectations that citizens have for postwar democracy, with adverse consequences for political participation. I demonstrate support for this argument using a mixed methods approach, combining qualitative interviews with census, voting, and Afrobarometer survey data. I leverage a difference-in-differences identification strategy to causally identify the negative impact of conflict on human capital for a generation of young adults, and on the downstream consequences of disruptions in education on political participation. Results indicate that children who were of school age during the civil war are differentially less likely to have any formal schooling by the end of the war. I further find that educational deficiencies disproportionately decrease postwar job prospects, breeding resentment against the newly elected government. This extends to political participation: those who lost out on educational opportunities due to war exhibit lower political engagement and less desire to engage with democratic processes.Item Open Access MCR toolkit: A GPU-based toolkit for multi-channel reconstruction of preclinical and clinical x-ray CT data.(Medical physics, 2023-06) Clark, Darin P; Badea, Cristian TBackground
The advancement of x-ray CT into the domains of photon counting spectral imaging and dynamic cardiac and perfusion imaging has created many new challenges and opportunities for clinicians and researchers. To address challenges such as dose constraints and scanning times while capitalizing on opportunities such as multi-contrast imaging and low-dose coronary angiography, these multi-channel imaging applications require a new generation of CT reconstruction tools. These new tools should exploit the relationships between imaging channels during reconstruction to set new image quality standards while serving as a platform for direct translation between the preclinical and clinical domains.Purpose
We outline and demonstrate a new Multi-Channel Reconstruction (MCR) Toolkit for GPU-based analytical and iterative reconstruction of preclinical and clinical multi-energy and dynamic x-ray CT data. To promote open science, open-source distribution of the Toolkit will coincide with the release of this publication (GPL v3; gitlab.oit.duke.edu/dpc18/mcr-toolkit-public).Methods
The MCR Toolkit source code is implemented in C/C++ and NVIDIA's CUDA GPU programming interface, with scripting support from MATLAB and Python. The Toolkit implements matched, separable footprint CT reconstruction operators for projection and backprojection in two geometries: planar, cone-beam CT (CBCT) and 3rd generation, cylindrical multi-detector row CT (MDCT). Analytical reconstruction is performed using filtered backprojection (FBP) for circular CBCT, weighted FBP (WFBP) for helical CBCT, and cone-parallel projection rebinning followed by WFBP for MDCT. Arbitrary combinations of energy and temporal channels are iteratively reconstructed under a generalized multi-channel signal model for joint reconstruction. We solve this generalized model algebraically using the split Bregman optimization method and the BiCGSTAB(l) linear solver interchangeably for both CBCT and MDCT data. Rank-sparse kernel regression (RSKR) and patch-based singular value thresholding (pSVT) are used to regularize the energy and time dimensions, respectively. Under a Gaussian noise model, regularization parameters are estimated automatically from the input data, dramatically reducing algorithm complexity for end users. Multi-GPU parallelization of the reconstruction operators is supported to manage reconstruction times.Results
Denoising with RSKR and pSVT and post-reconstruction material decomposition are illustrated with preclinical and clinical cardiac photon-counting (PC)CT data. A digital MOBY mouse phantom with cardiac motion is used to illustrate single energy (SE), multi-energy (ME), time resolved (TR), and combined multi-energy and time-resolved (METR) helical, CBCT reconstruction. A fixed set of projection data is used across all reconstruction cases to demonstrate the Toolkit's robustness to increasing data dimensionality. Identical reconstruction code is applied to in vivo cardiac PCCT data acquired in a mouse model of atherosclerosis (METR). Clinical cardiac CT reconstruction is illustrated using the XCAT phantom and the DukeSim CT simulator, while dual-source, dual-energy CT reconstruction is illustrated for data acquired with a Siemens Flash scanner. Benchmarking results with NVIDIA RTX 8000 GPU hardware demonstrate 61%-99% efficiency in scaling computation from one to four GPUs for these reconstruction problems.Conclusions
The MCR Toolkit provides a robust solution for temporal and spectral x-ray CT reconstruction problems and was built from the ground up to facilitate translation of CT research and development between preclinical and clinical applications.Item Open Access Super-resolution method for arbitrary retrospective sampling in fluorescence tomography with raster scanning photodetectors.(Proc SPIE Int Soc Opt Eng, 2013-03-22) Zhang, XiaofengDense spatial sampling is required in high-resolution optical imaging and many other biomedical optical imaging methods, such as diffuse optical imaging. Arrayed photodetectors, in particular charge coupled device cameras are commonly used mainly because of their high pixel count. Nonetheless, discrete-element photodetectors, such as photomultiplier tubes, are often desirable in many performance-demanding imaging applications. However, utilization of the discrete-element photodetectors typically requires raster scan to achieve arbitrary retrospective sampling with high density. Care must be taken in using the relatively large sensitive areas of discrete-element photodetectors to densely sample the image plane. In addition, off-line data analysis and image reconstruction often require full-field sampling. Pixel-by-pixel scanning is not only slow but also unnecessary in diffusion-limited imaging. We propose a super-resolution method that can recover the finer features of an image sampled with a coarse-scale sensor. This generalpurpose method was established on the spatial transfer function of the photodetector-lens system, and achieved super-resolution by inversion of this linear transfer function. Regularized optimization algorithms were used to achieve optimized deconvolution. Compared to the uncorrected blurred image, the proposed super-resolution method significantly improved image quality in terms of resolution and quantitation. Using this reconstruction method, the acquisition speed with a scanning photodetector can be dramatically improved without significantly sacrificing sampling density or flexibility.Item Open Access Use of multiple rods and proximal junctional kyphosis in adult spinal deformity surgery.(Journal of neurosurgery. Spine, 2023-06) Ye, Jichao; Gupta, Sachin; Farooqi, Ali S; Yin, Tsung-Cheng; Soroceanu, Alex; Schwab, Frank J; Lafage, Virginie; Kelly, Michael P; Kebaish, Khaled; Hostin, Richard; Gum, Jeffrey L; Smith, Justin S; Shaffrey, Christopher I; Scheer, Justin K; Protopsaltis, Themistocles S; Passias, Peter G; Klineberg, Eric O; Kim, Han Jo; Hart, Robert A; Hamilton, D Kojo; Ames, Christopher P; Gupta, Munish CObjective
Multiple rods are utilized in adult spinal deformity (ASD) surgery to increase construct stiffness. However, the impact of multiple rods on proximal junctional kyphosis (PJK) is not well established. This study aimed to investigate the impact of multiple rods on PJK incidence in ASD patients.Methods
ASD patients from a prospective multicenter database with a minimum follow-up of 1 year were retrospectively reviewed. Clinical and radiographic data were collected preoperatively, at 6 weeks postoperatively, at 6 months postoperatively, at 1 year postoperatively, and at every subsequent year postoperatively. PJK was defined as a kyphotic increase of > 10° in the Cobb angle from the upper instrumented vertebra (UIV) to UIV+2 as compared with preoperative values. Demographic data, radiographic parameters, and PJK incidence were compared between the multirod and dual-rod patient cohorts. PJK-free survival analysis was performed using Cox regression to control for demographic characteristics, comorbidities, level of fusion, and radiographic parameters.Results
Overall, 307/1300 (23.62%) cases utilized multiple rods. Cases with multiple rods were more likely to be revisions (68.4% vs 46.5%, p < 0.001), to be posterior only (80.7% vs 61.5%, p < 0.001), involve more levels of fusion (mean 11.73 vs 10.60, p < 0.001), and include 3-column osteotomy (42.9% vs 17.1%, p < 0.001). Patients with multiple rods also had greater preoperative pelvic retroversion (mean pelvic tilt 27.95° vs 23.58°, p < 0.001), greater thoracolumbar junction kyphosis (-15.9° vs -11.9°, p = 0.001), and more severe sagittal malalignment (C7-S1 sagittal vertical axis 99.76 mm vs 62.23 mm, p < 0.001), all of which corrected postoperatively. Patients with multiple rods had similar incidence rates of PJK (58.6% vs 58.1%) and revision surgery (13.0% vs 17.7%). The PJK-free survival analysis demonstrated equivalent PJK-free survival durations among the patients with multiple rods (HR 0.889, 95% CI 0.745-1.062, p = 0.195) after controlling for demographic and radiographic parameters. Further stratification based on implant metal type demonstrated noninferior PJK incidence rates with multiple rods in the titanium (57.1% vs 54.6%, p = 0.858), cobalt chrome (60.5% vs 58.7%, p = 0.646), and stainless steel (20% vs 63.7%, p = 0.008) cohorts.Conclusions
Multirod constructs for ASD are most frequently utilized in revision, long-level reconstructions with 3-column osteotomy. The use of multiple rods in ASD surgery does not result in an increased incidence of PJK and is not affected by rod metal type.