Single fluoroscopic image based 2D/3D reconstruction of a scaled, patient-specific vertebral model

Purpose Accurate three-dimensional (3D) models of lumbar vertebrae can enable image-based 3D kinematic analysis. The common approach to derive 3D models is by direct segmentation of CT or MRI datasets. However, these have the disadvantages that they are expensive, timeconsuming and/or induce high-radiation doses to the patient. In this study, we present a technique to automatically reconstruct a scaled 3D lumbar vertebral model from a single two-dimensional (2D) lateral fluoroscopic image. Methods Our technique is based on a hybrid 2D/3D deformable registration strategy combining a landmark-to-ray registration with a statistical shape model-based 2D/3D reconstruction scheme. Fig. 1 shows different stages of the reconstruction process. Four cadaveric lumbar spine segments (total twelve lumbar vertebrae) were used to validate the technique. To evaluate the reconstruction accuracy, the surface models reconstructed from the lateral fluoroscopic images were compared to the associated ground truth data derived from a 3D CT-scan reconstruction technique. For each case, a surface-based matching was first used to recover the scale and the rigid transformation between the reconstructed surface model Results Our technique could successfully reconstruct 3D surface models of all twelve vertebrae. After recovering the scale and the rigid transformation between the reconstructed surface models and the ground truth models, the average error of the 2D/3D surface model reconstruction over the twelve lumbar vertebrae was found to be 1.0 mm. The errors of reconstructing surface models of all twelve vertebrae are shown in Fig. 2. It was found that the mean errors of the reconstructed surface models in comparison to their associated ground truths after iterative scaled rigid registrations ranged from 0.7 mm to 1.3 mm and the rootmean squared (RMS) errors ranged from 1.0 mm to 1.7 mm. The average mean reconstruction error was found to be 1.0 mm. Conclusion An accurate, scaled 3D reconstruction of the lumbar vertebra can be obtained from a single lateral fluoroscopic image using a statistical shape model based 2D/3D reconstruction technique. Future work will focus on applying the reconstructed model for 3D kinematic analysis of lumbar vertebrae, an extension of our previously-reported imagebased kinematic analysis. The developed method also has potential applications in surgical planning and navigation.

ECM versus ICP for point registration

Iterative Closest Point (ICP) is a widely exploited method for point registration that is based on binary point-to-point assignments, whereas the Expectation Conditional Maximization (ECM) algorithm tries to solve the problem of point registration within the framework of maximum likelihood with point-to-cluster matching. In this paper, by fulfilling the implementation of both algorithms as well as conducting experiments in a scenario where dozens of model points must be registered with thousands of observation points on a pelvis model, we investigated and compared the performance (e.g. accuracy and robustness) of both ICP and ECM for point registration in cases without noise and with Gaussian white noise. The experiment results reveal that the ECM method is much less sensitive to initialization and is able to achieve more consistent estimations of the transformation parameters than the ICP algorithm, since the latter easily sinks into local minima and leads to quite different registration results with respect to different initializations. Both algorithms can reach the high registration accuracy at the same level, however, the ICP method usually requires an appropriate initialization to converge globally. In the presence of Gaussian white noise, it is observed in experiments that ECM is less efficient but more robust than ICP.

Generalized eMC implementation for Monte Carlo dose calculation of electron beams from different machine types

The electron Monte Carlo (eMC) dose calculation algorithm available in the Eclipse treatment planning system (Varian Medical Systems) is based on the macro MC method and uses a beam model applicable to Varian linear accelerators. This leads to limitations in accuracy if eMC is applied to non-Varian machines. In this work eMC is generalized to also allow accurate dose calculations for electron beams from Elekta and Siemens accelerators. First, changes made in the previous study to use eMC for low electron beam energies of Varian accelerators are applied. Then, a generalized beam model is developed using a main electron source and a main photon source representing electrons and photons from the scattering foil, respectively, an edge source of electrons, a transmission source of photons and a line source of electrons and photons representing the particles from the scrapers or inserts and head scatter radiation. Regarding the macro MC dose calculation algorithm, the transport code of the secondary particles is improved. The macro MC dose calculations are validated with corresponding dose calculations using EGSnrc in homogeneous and inhomogeneous phantoms. The validation of the generalized eMC is carried out by comparing calculated and measured dose distributions in water for Varian, Elekta and Siemens machines for a variety of beam energies, applicator sizes and SSDs. The comparisons are performed in units of cGy per MU. Overall, a general agreement between calculated and measured dose distributions for all machine types and all combinations of parameters investigated is found to be within 2% or 2 mm. The results of the dose comparisons suggest that the generalized eMC is now suitable to calculate dose distributions for Varian, Elekta and Siemens linear accelerators with sufficient accuracy in the range of the investigated combinations of beam energies, applicator sizes and SSDs.

A Computational Model for Processing Lexical Information"

The group analysed some syntactic and phonological phenomena that presuppose the existence of interrelated components within the lexicon, which motivate the assumption that there are some sublexicons within the global lexicon of a speaker. This result is confirmed by experimental findings in neurolinguistics. Hungarian speaking agrammatic aphasics were tested in several ways, the results showing that the sublexicon of closed-class lexical items provides a highly automated complex device for processing surface sentence structure. Analysing Hungarian ellipsis data from a semantic-syntactic aspect, the group established that the lexicon is best conceived of being as split into at least two main sublexicons: the store of semantic-syntactic feature bundles and a separate store of sound forms. On this basis they proposed a format for representing open-class lexical items whose meanings are connected via certain semantic relations. They also proposed a new classification of verbs to account for the contribution of the aspectual reading of the sentence depending on the referential type of the argument, and a new account of the syntactic and semantic behaviour of aspectual prefixes. The partitioned sets of lexical items are sublexicons on phonological grounds. These sublexicons differ in terms of phonotactic grammaticality. The degrees of phonotactic grammaticality are tied up with the problem of psychological reality, of how many degrees of this native speakers are sensitive to. The group developed a hierarchical construction network as an extension of the original General Inheritance Network formalism and this framework was then used as a platform for the implementation of the grammar fragments.

Squared Extrapolation Methods (SQUAREM): A New Class of Simple and Efficient Numerical Schemes for Accelerating the Convergence of the EM Algorithm

We derive a new class of iterative schemes for accelerating the convergence of the EM algorithm, by exploiting the connection between fixed point iterations and extrapolation methods. First, we present a general formulation of one-step iterative schemes, which are obtained by cycling with the extrapolation methods. We, then square the one-step schemes to obtain the new class of methods, which we call SQUAREM. Squaring a one-step iterative scheme is simply applying it twice within each cycle of the extrapolation method. Here we focus on the first order or rank-one extrapolation methods for two reasons, (1) simplicity, and (2) computational efficiency. In particular, we study two first order extrapolation methods, the reduced rank extrapolation (RRE1) and minimal polynomial extrapolation (MPE1). The convergence of the new schemes, both one-step and squared, is non-monotonic with respect to the residual norm. The first order one-step and SQUAREM schemes are linearly convergent, like the EM algorithm but they have a faster rate of convergence. We demonstrate, through five different examples, the effectiveness of the first order SQUAREM schemes, SqRRE1 and SqMPE1, in accelerating the EM algorithm. The SQUAREM schemes are also shown to be vastly superior to their one-step counterparts, RRE1 and MPE1, in terms of computational efficiency. The proposed extrapolation schemes can fail due to the numerical problems of stagnation and near breakdown. We have developed a new hybrid iterative scheme that combines the RRE1 and MPE1 schemes in such a manner that it overcomes both stagnation and near breakdown. The squared first order hybrid scheme, SqHyb1, emerges as the iterative scheme of choice based on our numerical experiments. It combines the fast convergence of the SqMPE1, while avoiding near breakdowns, with the stability of SqRRE1, while avoiding stagnations. The SQUAREM methods can be incorporated very easily into an existing EM algorithm. They only require the basic EM step for their implementation and do not require any other auxiliary quantities such as the complete data log likelihood, and its gradient or hessian. They are an attractive option in problems with a very large number of parameters, and in problems where the statistical model is complex, the EM algorithm is slow and each EM step is computationally demanding.

Reconstruction of patient-specific 3D bone surface from 2D calibrated fluoroscopic images and point distribution model

Reconstruction of patient-specific 3D bone surface from 2D calibrated fluoroscopic images and a point distribution model is discussed. We present a 2D/3D reconstruction scheme combining statistical extrapolation and regularized shape deformation with an iterative image-to-model correspondence establishing algorithm, and show its application to reconstruct the surface of proximal femur. The image-to-model correspondence is established using a non-rigid 2D point matching process, which iteratively uses a symmetric injective nearest-neighbor mapping operator and 2D thin-plate splines based deformation to find a fraction of best matched 2D point pairs between features detected from the fluoroscopic images and those extracted from the 3D model. The obtained 2D point pairs are then used to set up a set of 3D point pairs such that we turn a 2D/3D reconstruction problem to a 3D/3D one. We designed and conducted experiments on 11 cadaveric femurs to validate the present reconstruction scheme. An average mean reconstruction error of 1.2 mm was found when two fluoroscopic images were used for each bone. It decreased to 1.0 mm when three fluoroscopic images were used.

Monte Carlo source model for photon beam radiotherapy: photon source characteristics

A major barrier to widespread clinical implementation of Monte Carlo dose calculation is the difficulty in characterizing the radiation source within a generalized source model. This work aims to develop a generalized three-component source model (target, primary collimator, flattening filter) for 6- and 18-MV photon beams that match full phase-space data (PSD). Subsource by subsource comparison of dose distributions, using either source PSD or the source model as input, allows accurate source characterization and has the potential to ease the commissioning procedure, since it is possible to obtain information about which subsource needs to be tuned. This source model is unique in that, compared to previous source models, it retains additional correlations among PS variables, which improves accuracy at nonstandard source-to-surface distances (SSDs). In our study, three-dimensional (3D) dose calculations were performed for SSDs ranging from 50 to 200 cm and for field sizes from 1 x 1 to 30 x 30 cm2 as well as a 10 x 10 cm2 field 5 cm off axis in each direction. The 3D dose distributions, using either full PSD or the source model as input, were compared in terms of dose-difference and distance-to-agreement. With this model, over 99% of the voxels agreed within +/-1% or 1 mm for the target, within 2% or 2 mm for the primary collimator, and within +/-2.5% or 2 mm for the flattening filter in all cases studied. For the dose distributions, 99% of the dose voxels agreed within 1% or 1 mm when the combined source model-including a charged particle source and the full PSD as input-was used. The accurate and general characterization of each photon source and knowledge of the subsource dose distributions should facilitate source model commissioning procedures by allowing scaling the histogram distributions representing the subsources to be tuned.

Monte Carlo simulation of a dynamic MLC: implementation and applications

PURPOSE: Study of behavior and influence of a multileaf collimator (MLC) on dose calculation, verification, and portal energy spectra in the case of intensity-modulated fields obtained with a step-and-shoot or a dynamic technique. METHODS: The 80-leaf MLC for the Varian Clinac 2300 C/D was implemented in a previously developed Monte Carlo (MC) based multiple source model (MSM) for a 6 MV photon beam. Using this model and the MC program GEANT, dose distributions, energy fluence maps and energy spectra at different portal planes were calculated for three different MLC applications. RESULTS: The comparison of MC-calculated dose distributions in the phantom and portal plane, with those measured with films showed an agreement within 3% and 1.5 mm for all cases studied. The deviations mainly occur in the extremes of the intensity modulation. The MC method allows to investigate, among other aspects, dose components, energy fluence maps, tongue-and-groove effects and energy spectra at portal planes. CONCLUSION: The MSM together with the implementation of the MLC is appropriate for a number of investigations in intensity-modulated radiation therapy (IMRT).

Experimental model to evaluate in vivo and in vitro cartilage MR imaging by means of histological analyses

OBJECTIVES: Implementation of an experimental model to compare cartilage MR imaging by means of histological analyses. MATERIAL AND METHODS: MRI was obtained from 4 patients expecting total knee replacement at 1.5 and/or 3T prior surgery. The timeframe between pre-op MRI and knee replacement was within two days. Resected cartilage-bone samples were tagged with Ethi((R))-pins to reproduce the histological cutting course. Pre-operative scanning at 1.5T included following parameters for fast low angle shot (FLASH: TR/TE/FA=33ms/6ms/30 degrees , BW=110kHz, 120mmx120mm FOV, 256x256 matrix, 0.65mm slice-thickness) and double echo steady state (DESS: TR/TE/FA=23.7ms/6.9ms/40 degrees , BW=130kHz, 120x120mm FOV, 256x256 matrix, 0.65mm slice-thickness). At 3T, scan parameters were: FLASH (TR/TE/FA=12.2ms/5.1ms/10 degrees , BW=130kHz, 170x170mm FOV, 320x320, 0.5mm slice-thickness) and DESS (TR/TE/FA=15.6ms/4.5ms/25 degrees , BW=200kHz, 135mmx150mm FOV, 288x320matrix, 0.5mm slice-thickness). Imaging of the specimens was done the same day at 1.5T. MRI (Noyes) and histological (Mankin) score scales were correlated using the paired t-test. Sensitivity and specificity for the detection of different grades of cartilage degeneration were assessed. Inter-reader and intra-reader reliability was determined using Kappa analysis. RESULTS: Low correlation (sensitivity, specificity) was found for both sequences in normal to mild Mankin grades. Only moderate to severe changes were diagnosed with higher significance and specificity. The use of higher field-strengths was advantageous for both protocols with sensitivity values ranging from 13.6% to 93.3% (FLASH) and 20.5% to 96.2% (DESS). Kappa values ranged from 0.488 to 0.944. CONCLUSIONS: Correlating MR images with continuous histological slices was feasible by using three-dimensional imaging, multi-planar-reformat and marker pins. The capability of diagnosing early cartilage changes with high accuracy could not be proven for both FLASH and DESS.

Model to describe the mode I fracture of steel fiber reinforced ultra-high performance concrete

Ultra-high performance fiber reinforced concrete (UHPFRC) has arisen from the implementation of a variety of concrete engineering and materials science concepts developed over the last century. This material offers superior strength, serviceability, and durability over its conventional counterparts. One of the most important differences for UHPFRC over other concrete materials is its ability to resist fracture through the use of randomly dispersed discontinuous fibers and improvements to the fiber-matrix bond. Of particular interest is the materials ability to achieve higher loads after first crack, as well as its high fracture toughness. In this research, a study of the fracture behavior of UHPFRC with steel fibers was conducted to look at the effect of several parameters related to the fracture behavior and to develop a fracture model based on a non-linear curve fit of the data. To determine this, a series of three-point bending tests were performed on various single edge notched prisms (SENPs). Compression tests were also performed for quality assurance. Testing was conducted on specimens of different cross-sections, span/depth (S/D) ratios, curing regimes, ages, and fiber contents. By comparing the results from prisms of different sizes this study examines the weakening mechanism due to the size effect. Furthermore, by employing the concept of fracture energy it was possible to obtain a comparison of the fracture toughness and ductility. The model was determined based on a fit to P-w fracture curves, which was cross referenced for comparability to the results. Once obtained the model was then compared to the models proposed by the AFGC in the 2003 and to the ACI 544 model for conventional fiber reinforced concretes.

Parameter estimation for transformer modeling

Large Power transformers, an aging and vulnerable part of our energy infrastructure, are at choke points in the grid and are key to reliability and security. Damage or destruction due to vandalism, misoperation, or other unexpected events is of great concern, given replacement costs upward of $2M and lead time of 12 months. Transient overvoltages can cause great damage and there is much interest in improving computer simulation models to correctly predict and avoid the consequences. EMTP (the Electromagnetic Transients Program) has been developed for computer simulation of power system transients. Component models for most equipment have been developed and benchmarked. Power transformers would appear to be simple. However, due to their nonlinear and frequency-dependent behaviors, they can be one of the most complex system components to model. It is imperative that the applied models be appropriate for the range of frequencies and excitation levels that the system experiences. Thus, transformer modeling is not a mature field and newer improved models must be made available. In this work, improved topologically-correct duality-based models are developed for three-phase autotransformers having five-legged, three-legged, and shell-form cores. The main problem in the implementation of detailed models is the lack of complete and reliable data, as no international standard suggests how to measure and calculate parameters. Therefore, parameter estimation methods are developed here to determine the parameters of a given model in cases where available information is incomplete. The transformer nameplate data is required and relative physical dimensions of the core are estimated. The models include a separate representation of each segment of the core, including hysteresis of the core, λ-i saturation characteristic, capacitive effects, and frequency dependency of winding resistance and core loss. Steady-state excitation, and de-energization and re-energization transients are simulated and compared with an earlier-developed BCTRAN-based model. Black start energization cases are also simulated as a means of model evaluation and compared with actual event records. The simulated results using the model developed here are reasonable and more correct than those of the BCTRAN-based model. Simulation accuracy is dependent on the accuracy of the equipment model and its parameters. This work is significant in that it advances existing parameter estimation methods in cases where the available data and measurements are incomplete. The accuracy of EMTP simulation for power systems including three-phase autotransformers is thus enhanced. Theoretical results obtained from this work provide a sound foundation for development of transformer parameter estimation methods using engineering optimization. In addition, it should be possible to refine which information and measurement data are necessary for complete duality-based transformer models. To further refine and develop the models and transformer parameter estimation methods developed here, iterative full-scale laboratory tests using high-voltage and high-power three-phase transformer would be helpful.

Muffler characterization with implementation of the finite element method and experimental techniques

Determining how an exhaust system will perform acoustically before a prototype muffler is built can save the designer both a substantial amount of time and resources. In order to effectively use the simulation tools available it is important to understand what is the most effective tool for the intended purpose of analysis as well as how typical elements in an exhaust system affect muffler performance. An in-depth look at the available tools and their most beneficial uses are presented in this thesis. A full parametric study was conducted using the FEM method for typical muffler elements which was also correlated to experimental results. This thesis lays out the overall ground work on how to accurately predict sound pressure levels in the free field for an exhaust system with the engine properties included. The accuracy of the model is heavily dependent on the correct temperature profile of the model in addition to the accuracy of the source properties. These factors will be discussed in detail and methods for determining them will be presented. The secondary effects of mean flow, which affects both the acoustical wave propagation and the flow noise generation, will be discussed. Effective ways for predicting these secondary effects will be described. Experimental models will be tested on a flow rig that showcases these phenomena.

Ultraviolet digital imaging of volcanic plumes : implementation and application to magmatic processes at basaltic volcanoes

Magmatic volatiles play a crucial role in volcanism, from magma production at depth to generation of seismic phenomena to control of eruption style. Accordingly, many models of volcano dynamics rely heavily on behavior of such volatiles. Yet measurements of emission rates of volcanic gases have historically been limited, which has restricted model verification to processes on the order of days or longer. UV cameras are a recent advancement in the field of remote sensing of volcanic SO2 emissions. They offer enhanced temporal and spatial resolution over previous measurement techniques, but need development before they can be widely adopted and achieve the promise of integration with other geophysical datasets. Large datasets require a means by which to quickly and efficiently use imagery to calculate emission rates. We present a suite of programs designed to semi-automatically determine emission rates of SO2 from series of UV images. Extraction of high temporal resolution SO2 emission rates via this software facilitates comparison of gas data to geophysical data for the purposes of evaluating models of volcanic activity and has already proven useful at several volcanoes. Integrated UV camera and seismic measurements recorded in January 2009 at Fuego volcano, Guatemala, provide new insight into the system’s shallow conduit processes. High temporal resolution SO2 data reveal patterns of SO2 emission rate relative to explosions and seismic tremor that indicate tremor and degassing share a common source process. Progressive decreases in emission rate appear to represent inhibition of gas loss from magma as a result of rheological stiffening in the upper conduit. Measurements of emission rate from two closely-spaced vents, made possible by the high spatial resolution of the camera, help constrain this model. UV camera measurements at Kilauea volcano, Hawaii, in May of 2010 captured two occurrences of lava filling and draining within the summit vent. Accompanying high lava stands were diminished SO2 emission rates, decreased seismic and infrasonic tremor, minor deflation, and slowed lava lake surface velocity. Incorporation of UV camera data into the multi-parameter dataset gives credence to the likelihood of shallow gas accumulation as the cause of such events.

Implementation of MET/CBT 5 for adolescents

Implementation of effective substance abuse treatment programs in community settings is a high priority. The selection of a proven cost-effective model is a first step; however, difficulty arises when the model is imported into a community setting. The Center on Substance Abuse Treatment selected a brief substance abuse treatment program for adolescents, the MET/CBT-5 program, determined to be the most cost-effective protocol in the Cannabis Youth Treatment trial, for implementation in two cohorts of Effective Adolescent Treatment grantees. A qualitative investigation of the protocol implementation with nine sites in the second cohort chronicled adaptations made by grantees and prospects for sustainability. The study found that agencies introduced adaptations without seeming to be aware of potential effects on validity. In most sites, sessions were lengthened or added to accommodate individual client needs, address barriers to client participation, and provide consistency with current norms of treatment. Implications for fidelity of future implementation projects are addressed.

STATE-AND-TRANSITION MODELING AND ADAPTIVE MANAGEMENT: TOOLS FOR FUTURE CO-DEVELOPMENT OF MADAGASCAR’S NATURAL RESOURCES AND PEOPLE

Madagascar’s terrestrial and aquatic ecosystems have long supported a unique set of ecological communities, many of whom are endemic to the tropical island. Those same ecosystems have been a source of valuable natural resources to some of the poorest people in the world. Nevertheless, with pride, ingenuity and resourcefulness, the Malagasy people of the southwest coast, being of Vezo identity, subsist with low development fishing techniques aimed at an increasingly threatened host of aquatic seascapes. Mangroves, sea grass bed, and coral reefs of the region are under increased pressure from the general populace for both food provisions and support of economic opportunity. Besides purveyors and extractors, the coastal waters are also subject to a number of natural stressors, including cyclones and invasive, predator species of both flora and fauna. In addition, the aquatic ecosystems of the region are undergoing increased nutrient and sediment runoff due, in part, to Madagascar’s heavy reliance on land for agricultural purposes (Scales, 2011). Moreover, its coastal waters, like so many throughout the world, have been proven to be warming at an alarming rate over the past few decades. In recognizing the intimate interconnectedness of the both the social and ecological systems, conservation organizations have invoked a host of complimentary conservation and social development efforts with the dual aim of preserving or restoring the health of both the coastal ecosystems and the people of the region. This paper provides a way of thinking more holistically about the social-ecological system within a resiliency frame of understanding. Secondly, it applies a platform known as state-and-transition modeling to give form to the process. State-and-transition modeling is an iterative investigation into the physical makeup of a system of study as well as the boundaries and influences on that state, and has been used in restorative ecology for more than a decade. Lastly, that model is sited within an adaptive management scheme that provides a structured, cyclical, objective-oriented process for testing stakeholders cognitive understanding of the ecosystem through a pragmatic implementation and monitoring a host of small-scale interventions developed as part of the adaptive management process. Throughout, evidence of the application of the theories and frameworks are offered, with every effort made to retool conservation-minded development practitioners with a comprehensive strategy for addressing the increasingly fragile social-ecological systems of southwest Madagascar. It is offered, in conclusion, that the seascapes of the region would be an excellent case study worthy of future application of state-and-transition modeling and adaptive management as frameworks for conservation-minded development practitioners whose multiple projects, each with its own objective, have been implemented with a single goal in mind: preserve and protect the state of the supporting environment while providing for the basic needs of the local Malagasy people.