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WE-G-18A-04: 3D Dictionary Learning Based Statistical Iterative Reconstruction for Low-Dose Cone Beam CT Imaging

Purpose: To develop a 3D dictionary learning based statistical reconstruction algorithm on graphic processing units (GPU), to improve the quality of low-dose cone beam CT (CBCT) imaging with high efficiency. Methods: A 3D dictionary containing 256 small volumes (atoms) of 3x3x3 voxels was trained from a high quality volume image. During reconstruction, we utilized a Cholesky decomposition based orthogonal matching pursuit algorithm to find a sparse representation on this dictionary basis of each patch in the reconstructed image, in order to regularize the image quality. To accelerate the time-consuming sparse coding in the 3D case, we implemented our algorithm in a parallel fashion by taking advantage of the tremendous computational power of GPU. Evaluations are performed based on a head-neck patient case. FDK reconstruction with full dataset of 364 projections is used as the reference. We compared the proposed 3D dictionary learning based method with a tight frame (TF) based one using a subset data of 121 projections. The image qualities under different resolutions in z-direction, with or without statistical weighting are also studied. Results: Compared to the TF-based CBCT reconstruction, our experiments indicated that 3D dictionary learning based CBCT reconstruction is able to recover finer structures, to remove more streaking artifacts, and is less susceptible to blocky artifacts. It is also observed that statistical reconstruction approach is sensitive to inconsistency between the forward and backward projection operations in parallel computing. Using high a spatial resolution along z direction helps improving the algorithm robustness. Conclusion: 3D dictionary learning based CBCT reconstruction algorithm is able to sense the structural information while suppressing noise, and hence to achieve high quality reconstruction. The GPU realization of the whole algorithm offers a significant efficiency enhancement, making this algorithm more feasible for potential clinical application. A high zresolution is preferred to stabilize statistical iterative reconstruction. This work was supported in part by NIH(1R01CA154747-01), NSFC((No. 61172163), Research Fund for the Doctoral Program of Higher Education of China (No. 20110201110011), China Scholarship Council.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Global Sensitivity Analysis for Statistical Model Parameters

Global sensitivity analysis (GSA) is typically used to analyze the influence of uncertain parameters in mathematical models and simulations. In principle, tools from GSA may be extended to analyze the influence of parameters in statistical models. Such analyses may enable reduced or parsimonious modeling and greater predictive capability. Yet, difficulties such as parameter correlation, model stochasticity, multivariate model output, and unknown parameter distributions prohibit a direct application of GSA tools to statistical models. By leveraging a loss function associated with the statistical model, we introduce a novel framework to address these difficulties and enable efficient GSA for statistical model parameters. Theoretical and computational properties are considered and hihglighted on a synthetic example. The framework is applied to a Gaussian process model from the literature, which depends on 95 parameters. Noninfluential parameters are discovered through GSA, and a reduced model with equal or stronger predictive capability is constructed by using only 79 parameters.

97 MATHEMATICS AND COMPUTING↗

Convective Transition Statistics over Tropical Oceans for Climate Model Diagnostics: Observational Baseline

Convective transition statistics, which describe the relation between column-integrated water vapor (CWV) and precipitation, are compiled over tropical oceans using satellite and ARM site measurements to quantify the temperature and resolution dependence of the precipitation–CWV relation at fast time scales relevant to convection. At these time scales, and for precipitation especially, uncertainties associated with observational systems must be addressed by examining features with a variety of instrumentation and identifying robust behaviors versus instrument sensitivity at high rain rates. Here the sharp pickup in precipitation as CWV exceeds a certain critical threshold is found to be insensitive to spatial resolution, with convective onset occurring at higher CWV but at lower column relative humidity as bulk tropospheric temperature increases. Mean tropospheric temperature profiles conditioned on precipitation show vertically coherent structure across a wide range of temperature, reaffirming the use of a bulk temperature measure in defining the convective transition statistics. The joint probability distribution of CWV and precipitation develops a peak probability at low precipitation for CWV above critical, with rapidly decreasing probability of high precipitation below and near critical, and exhibits systematic changes under spatial averaging. The precipitation pickup with CWV is reasonably insensitive to time averaging up to several hours but is smoothed at daily time scales. This work demonstrates that CWV relative to critical serves as an effective predictor of precipitation with only minor geographic variations in the tropics, quantifies precipitation-related statistics subject to different spatial–temporal resolution, and provides a baseline for model comparison to apply these statistics as observational constraints on precipitation processes.

54 ENVIRONMENTAL SCIENCES↗

Convective Transition Statistics over Tropical Oceans for Climate Model Diagnostics: GCM Evaluation

To assess deep convective parameterizations in a variety of GCMs and examine the fast-time-scale convective transition, a set of statistics characterizing the pickup of precipitation as a function of column water vapor (CWV), PDFs and joint PDFs of CWV and precipitation, and the dependence of the moisture–precipitation relation on tropospheric temperature is evaluated using the hourly output of two versions of the GFDL Atmospheric Model, version 4 (AM4), NCAR CAM5 and superparameterized CAM (SPCAM). The 6-hourly output from the MJO Task Force (MJOTF)/GEWEX Atmospheric System Study (GASS) project is also analyzed. Contrasting statistics produced from individual models that primarily differ in representations of moist convection suggest that convective transition statistics can substantially distinguish differences in convective representation and its interaction with the large-scale flow, while models that differ only in spatial–temporal resolution, microphysics, or ocean–atmosphere coupling result in similar statistics. Most of the models simulate some version of the observed sharp increase in precipitation as CWV exceeds a critical value, as well as that convective onset occurs at higher CWV but at lower column RH as temperature increases. While some models quantitatively capture these observed features and associated probability distributions, considerable intermodel spread and departures from observations in various aspects of the precipitation–CWV relationship are noted. For instance, in many of the models, the transition from the low-CWV, nonprecipitating regime to the moist regime for CWV around and above critical is less abrupt than in observations. Additionally, some models overproduce drizzle at low CWV, and some require CWV higher than observed for strong precipitation. For many of the models, it is particularly challenging to simulate the probability distributions of CWV at high temperature.

54 ENVIRONMENTAL SCIENCES↗

In-Situ Statistical Analysis of Autotune Simulation Data using Graphical Processing Units

Developing accurate building energy simulation models to assist energy efficiency at speed and scale is one of the research goals of the Whole-Building and Community Integration group, which is a part of Building Technologies Research and Integration Center (BTRIC) at Oak Ridge National Laboratory (ORNL). The aim of the Autotune project is to speed up the automated calibration of building energy models to match measured utility or sensor data. The workflow of this project takes input parameters and runs EnergyPlus simulations on Oak Ridge Leadership Computing Facility’s (OLCF) computing resources such as Titan, the world’s second fastest supercomputer. Multiple simulations run in parallel on nodes having 16 processors each and a Graphics Processing Unit (GPU). Each node produces a 5.7 GB output file comprising 256 files from 64 simulations. Four types of output data covering monthly, daily, hourly, and 15- minute time steps for each annual simulation is produced. A total of 270TB+ of data has been produced. In this project, the simulation data is statistically analyzed in-situ using GPUs while annual simulations are being computed on the traditional processors. Titan, with its recent addition of 18,688 Compute Unified Device Architecture (CUDA) capable NVIDIA GPUs, has greatly extended its capability for massively parallel data processing. CUDA is used along with C/MPI to calculate statistical metrics such as sum, mean, variance, and standard deviation leveraging GPU acceleration. The workflow developed in this project produces statistical summaries of the data which reduces by multiple orders of magnitude the time and amount of data that needs to be stored. These statistical capabilities are anticipated to be useful for sensitivity analysis of EnergyPlus simulations

accelerators↗

Summary Statistics for LC_TA03_130719: Micro-CT Data Acquired at LLNL, Specimen 3 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, lithium carbonate (LC). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, LC_TA03_130719, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images 2 . The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗

Summary Statistics for TA_MP03_130620: Micro-CT Data Acquired at LLNL, Specimen 3 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, tartaric acid (TA). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, TA_MP03_130620, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images 2 . The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗

Summary Statistics for TA_MH03_130828: Micro-CT Data Acquired at LLNL, Specimen 3 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, tartaric acid (TA). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, TA_MH03_130828, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images. The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗

Summary Statistics for TA_MH01_130826: Micro-CT Data Acquired at LLNL, Specimen 1 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, tartaric acid (TA). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, TA_MH01_130826, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images. The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗

Summary Statistics for TA_MH02_130827: Micro-CT Data Acquired at LLNL, Specimen 2 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, tartaric acid (TA). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, TA_MH03_130827, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images. The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗

Summary Statistics for TA_MC03_130806: Micro-CT Data Acquired at LLNL, Specimen 3 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, tartaric acid (TA). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, TA_MC03_130806, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images. The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗

Summary Statistics for TA_MC02_130701: Micro-CT Data Acquired at LLNL, Specimen 2 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, tartaric acid (TA). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, TA_MC02_130701, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images. The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗

Summary Statistics for TA_ST01_130731: Micro-CT Data Acquired at LLNL, Specimen 1 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, tartaric acid (TA). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, TA_ST01_130731, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images. The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗

Summary Statistics for TA_SH02_130820: Micro-CT Data Acquired at LLNL, Specimen 2 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, tartaric acid (TA). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, TA_SH02_130820, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images. The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗

Summary Statistics for TA_MT03_130730: Micro-CT Data Acquired at LLNL, Specimen 3 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, tartaric acid (TA). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, TA_MT03_130730, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images. The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗

Summary Statistics for TA_SH01_130819: Micro-CT Data Acquired at LLNL, Specimen 1 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, tartaric acid (TA). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, TA_SH01_130819, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images. The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗

Summary Statistics for TA_MT01_130725: Micro-CT Data Acquired at LLNL, Specimen 1 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, tartaric acid (TA). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, TA_MT01_130725, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images. The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗

Summary Statistics for TA_MT02_130729: Micro-CT Data Acquired at LLNL, Specimen 2 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, tartaric acid (TA). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, TA_MT02_130729, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images. The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗