The Experts below are selected from a list of 312 Experts worldwide ranked by ideXlab platform

Timothy R. Ginn - One of the best experts on this subject based on the ideXlab platform.

  • Final Technical Report for DOE Award DE-FG02-07ER64403 [Modeling of Microbially Induced Calcite Precipitation for the Immobilization of Strontium-90 Using a Variable Velocity Streamtube Ensemble]
    2013
    Co-Authors: Timothy R. Ginn, T. S. Weathers
    Abstract:

    Biogeochemical modeling using PHREEQC2 and a streamtube ensemble approach is utilized to understand a well-to-well subsurface treatment system at the Vadose Zone Research Park (VZRP) near Idaho Falls, Idaho. Treatment involves in situ microbially-mediated ureolysis to induce calcite precipitation for the immobilization of strontium-90. PHREEQC2 is utilized to model the kinetically-controlled ureolysis and consequent calcite precipitation. Reaction kinetics, equilibrium phases, and cation exchange are used within PHREEQC2 to track pH and levels of calcium, ammonium, urea, and calcite precipitation over time, within a series of one-dimensional advective-dispersive transport paths creating a streamtube ensemble representation of the well-to-well transport. An understanding of the impact of physical heterogeneities within this radial flowfield is critical for remediation design; we address this via the streamtube approach: instead of depicting spatial extents of solutes in the subsurface we focus on their arrival distribution at the control well(s). Traditionally, each streamtube maintains uniform velocity; however in radial flow in homogeneous media, the velocity within any given streamtube is spatially-variable in a common way, being highest at the input and output wells and approaching a minimum at the midpoint between the wells. This idealized velocity variability is of significance in the case of ureolytically driven calcite precipitation. Streamtube velocity patterns for any particular configuration of injection and withdrawal wells are available as explicit calculations from more » potential theory, and also from particle tracking programs. To approximate the actual spatial distribution of velocity along Streamtubes, we assume idealized radial non-uniform velocity associated with homogeneous media. This is implemented in PHREEQC2 via a non-uniform spatial discretization within each streamtube that honors both the streamtube’s travel time and the idealized “fast-slow-fast” pattern of non-uniform velocity along the streamline. Breakthrough curves produced by each simulation are weighted by the path-respective flux fractions (obtained by deconvolution of tracer tests conducted at the VZRP) to obtain the flux-average of flow contributions to the observation well. « less

  • Stochastic-convective transport with nonlinear reaction and mixing: application to intermediate-scale experiments in aerobic biodegradation in saturated porous media
    Journal of Contaminant Hydrology, 2001
    Co-Authors: Timothy R. Ginn, Ellyn M. Murphy, Ashokkumar Chilakapati, Uma Seeboonruang
    Abstract:

    Aerobic biodegradation of benzoate by Pseudomonas cepacia sp. in a saturated heterogeneous porous medium was simulated using the stochastic-convective reaction (SCR) approach. A laboratory flow cell was randomly packed with low permeability silt-size inclusions in a high permeability sand matrix. In the SCR upscaling approach, the characteristics of the flow field are determined by the breakthrough of a conservative tracer. Spatial information on the actual location of the heterogeneities is not used. The mass balance equations governing the nonlinear and multicomponent reactive transport are recast in terms of reactive transports in each of a finite number of discrete Streamtubes. The streamtube ensemble members represent transport via a steady constant average velocity per streamtube and a conventional Fickian dispersion term, and their contributions to the observed breakthroughs are determined by flux-averaging the streamtube solute concentrations. The resulting simulations were compared to those from a high-resolution deterministic simulation of the reactive transport, and to alternative ensemble representations involving (i) effective Fickian travel time distribution function, (ii) purely convective streamtube transport, and (iii) streamtube ensemble subset simulations. The results of the SCR simulation compare favorably to that of a sophisticated high-resolution deterministic approach.

  • Stochastic-convective transport with nonlinear reactions and mixing: finite streamtube ensemble formulation for multicomponent reaction systems with intra-streamtube dispersion.
    Journal of contaminant hydrology, 2001
    Co-Authors: Timothy R. Ginn
    Abstract:

    An effective streamtube ensemble method is developed to upscale convective-dispersive transport with multicomponent nonlinear reactions in steady nonuniform flow. The transport is cast in terms of a finite ensemble of independent discrete Streamtubes that approximate convective transport along macroscopically averaged pathlines and dispersive transport longitudinally as microscopic mixing within Streamtubes. The representation of fate and transport via a finite ensemble of effective linear Streamtubes, allows the treatment of arbitrarily complex reaction systems involving both homogeneous and heterogeneous reactions, and longitudinal dispersive/diffusive mixing within Streamtubes. This allows the use of reactive-transport codes designed to solve such problems in an Eulerian framework, as opposed to reliance on closed-form (convolutional or canonical) expressions for reactive transport in exclusively convective Streamtubes. The approach requires both reactive-transport solutions for a representative ensemble of one-dimensional convective-dispersive-reactive Streamtubes and the distribution of flux over the streamtube ensemble variants, and it does not allow for lateral mixing between Streamtubes. Here, the only ensemble variant is travel time. The discussion details the way that the conventional Eulerian fate and transport model is converted first into an ensemble of transports along three-dimensional Streamtubes of unknown geometry, and then to approximate one-dimensional Streamtubes that are designed to honor the important global properties of the transport. Conditions under which such an 'equivalent' ensemble of one-dimensional Streamtubes are described. The breakthrough curve of a nonreactive tracer in the ensemble is expressed as a combined Volterra-Fredholm integral equation, which serves as the basis for estimation of the distribution of flux over the variant of the ensemble, travel time. Transient convective speed and the effects of errors in flux distributions are described, and the method is applied to a demonstration problem involving nonlinear multicomponent reaction kinetics and strongly nonuniform flow.

Bradford Navia - One of the best experts on this subject based on the ideXlab platform.

  • Quantitative Diffusion Tensor Imaging Tractography Metrics are Associated with Cognitive Performance Among HIV-Infected Patients
    Brain Imaging and Behavior, 2010
    Co-Authors: D. F. Tate, Song Zhang, David H. Laidlaw, R. H. Paul, Jared Conley, Kathryn Coop, Wenjin Zhou, Lynn E. Taylor, Timothy Flanigan, Bradford Navia
    Abstract:

    There have been many studies examining HIV-infection-related alterations of magnetic resonance imaging (MRI) diffusion metrics. However, examining scalar diffusion metrics ignores the orientation aspect of diffusion imaging, which can be captured with tractography. We examined five different tractography metrics obtained from global tractography maps (global tractography FA, average tube length, normalized number of Streamtubes, normalized weighted streamtube length, and normalized total number of tubes generated) for differences between HIV positive and negative patients and the association between the metrics and clinical variables of disease severity. We also examined the relationship between these metrics and cognitive performance across a wide range of cognitive domains for the HIV positive and negative patient groups separately. The results demonstrated a significant difference between the groups for global tractography FA ( t  = 2.13, p  = 0.04), but not for any of the other tractography metrics examined ( p -value range = 0.39 to 0.95). There were also several significant associations between the tractography metrics and cognitive performance (i.e., tapping rates, switching 1 and 2, verbal interference, mazes; r  ≥ 0.42) for HIV infected patients. In particular, associations were noted between tractography metrics, speed of processing, fine motor control/speed, and executive function for the HIV-infected patients. These findings suggest that tractography metrics capture clinically relevant information regarding cognitive performance among HIV infected patients and suggests the importance of subtle white matter changes in examining cognitive performance.

  • Quantitative Diffusion Tensor Imaging Tractography Metrics are Associated with Cognitive Performance Among HIV-Infected Patients
    2009
    Co-Authors: Bradford Navia, D. F. Tate, R. H. Paul, S. Zhang
    Abstract:

    Abstract There have been many studies examining HIVinfection-related alterations of magnetic resonance imaging (MRI) diffusion metrics. However, examining scalar diffusion metrics ignores the orientation aspect of diffusion imaging, which can be captured with tractography. We examined five different tractography metrics obtained from global tractography maps (global tractography FA, average tube length, normalized number of Streamtubes, normalized weighted streamtube length, and normalized total number of tubes generated) for differences between HIV positive and negative patients and the association between the metrics and clinical variables of disease severity. We also examined the relationship between these metrics and cognitive performance across a wide range of cognitive domains for the HIV positive and negative patient group

Carmo De Covas Santos - One of the best experts on this subject based on the ideXlab platform.

  • Modelo para analise de deslocamento miscivel no meio poroso usando a teoria dos canais de fluxo
    2017
    Co-Authors: Carmo De Covas Santos
    Abstract:

    Resumo: Este trabalho apresenta um modelo para análise de deslocamento miscível a dois componentes, em uma única fase, considerando reservatórios homogêneo e heterogêneo, e mobilidade total constante (M =1). Os canais de fluxo são gerados a partir da solução da equação diferencial parcial da Função Corrente. A discretização desta equação resulta num sistema matricial pentadiagonal, o qual é resolvido utilizando-se o método iterativo do Gradiente Conjugado com Precondicionador Diagonal. A Equação de Difusão-Convecção é definida para um canal de fluxo genérico e discretizada pelo método das diferenças finitas. A solução destaequação é então aplicada para os canais de fluxo calculados a partir da função corrente. O tratamento numérico da Equação de Difusão-Convecção usando o método de ponderação a montante estabiliza a solução, porém introduz erros de dispersão numérica. Uma modificação do esquema de Diminuição das Variações Totais (TVD) de segunda ordem, descrito para equações hiperbólicas, é utilizado para produzir soluções de melhor resolução. O Simulador numérico é validado com base no trabalho de Abaszadeh-Deghani e Brigham, 1982. Modelos heterogêneos são simulados para mostrar a influência da variação da permeabilidade no comportamento daslinhas de fluxo e na totalização das concentrações no poço produtorAbstract: This work describes a model for the analysis of a two-components, single phase miscible displacement, considering both homogeneous and heterogeneous reservoirs, and constant total mobility (M =1). The Streamtubes are computed from the solution of the partial differential equation of the Stream Function. The discretization of such equation results in a pentadiagonal matrix system, which is solved using the Conjugate Gradient methods with Diagonal Preconditioning. The Diffusion-Convection Equation is solved for each streamtube, using the finite-difference method. The numerical treatment of the Diffusion-Convection Equation usingupstream weithging method stabilizes the solution, but it introduces numerical dispersion. A modification of the methods of Total Variation Diminishing (TVD) of second order, described for hyperbolic equations, is used to produce solutions of better resolution. The numerical solution is validated againstthe work of Abaszadeh-Deghani and Brigham, 1982. Heterogeneous systems are simulated to show the infIuence of the penneability variations in the behavior of the Streamtubes, and in the computation of the concentrations in the producing wel

  • Modelo para analise de deslocamento miscivel no meio poroso usando a teoria dos canais de fluxo
    Universidade Estadual de Campinas. Faculdade de Engenharia Mecânica e Instituto de Geociências, 1998
    Co-Authors: Carmo De Covas Santos
    Abstract:

    Este trabalho apresenta um modelo para análise de deslocamento miscível a dois componentes, em uma única fase, considerando reservatórios homogêneo e heterogêneo, e mobilidade total constante (M =1). Os canais de fluxo são gerados a partir da solução da equação diferencial parcial da Função Corrente. A discretização desta equação resulta num sistema matricial pentadiagonal, o qual é resolvido utilizando-se o método iterativo do Gradiente Conjugado com Precondicionador Diagonal. A Equação de Difusão-Convecção é definida para um canal de fluxo genérico e discretizada pelo método das diferenças finitas. A solução desta equação é então aplicada para os canais de fluxo calculados a partir da função corrente. O tratamento numérico da Equação de Difusão-Convecção usando o método de ponderação a montante estabiliza a solução, porém introduz erros de dispersão numérica. Uma modificação do esquema de Diminuição das Variações Totais (TVD) de segunda ordem, descrito para equações hiperbólicas, é utilizado para produzir soluções de melhor resolução. O Simulador numérico é validado com base no trabalho de Abaszadeh-Deghani e Brigham, 1982. Modelos heterogêneos são simulados para mostrar a influência da variação da permeabilidade no comportamento das linhas de fluxo e na totalização das concentrações no poço produtorThis work describes a model for the analysis of a two-components, single phase miscible displacement, considering both homogeneous and heterogeneous reservoirs, and constant total mobility (M =1). The Streamtubes are computed from the solution of the partial differential equation of the Stream Function. The discretization of such equation results in a pentadiagonal matrix system, which is solved using the Conjugate Gradient methods with Diagonal Preconditioning. The Diffusion-Convection Equation is solved for each streamtube, using the finite-difference method. The numerical treatment of the Diffusion-Convection Equation using upstream weithging method stabilizes the solution, but it introduces numerical dispersion. A modification of the methods of Total Variation Diminishing (TVD) of second order, described for hyperbolic equations, is used to produce solutions of better resolution. The numerical solution is validated againstthe work of Abaszadeh-Deghani and Brigham, 1982. Heterogeneous systems are simulated to show the infIuence of the penneability variations in the behavior of the Streamtubes, and in the computation of the concentrations in the producing wel

Thomas A. Hewett - One of the best experts on this subject based on the ideXlab platform.

  • A Hybrid Streamtube Simulator Using A Semianalytical Method
    All Days, 2000
    Co-Authors: Munseok Baek, Thomas A. Hewett
    Abstract:

    Abstract A hybrid streamtube simulator is developed using a semianalytical method. This hybrid simulator applies to steady-state, incompressible, two-phase, field-scale problems, where the effects of gravity can be neglected. The underlying idea of the hybrid streamtube method is to decouple a large 3-D problem into multiple cross-sections along areal streamtube bundles. Using the calculations of cross-sections, the areal recovery is computed. This method is based on the assumption that the effects of a changing mobility field can be accounted for by using fixed streamtube geometries with updated flowrates. In each cross-section the semi-analytical method is applied, which uses the single-phase pressure distribution and the 1-D Buckley-Leverett solution along the streamtube. The distribution of pore volume along each streamtube is calculated by using the Time-Of-Flight method. This information and the pressure solution are used to calculate oil recovery by the semianalytical method. Unlike previous hybrid methods, the simulator developed uses a streamtube method in each cross-section. Due to the simple calculations and small arrays the method developed shows a very fast calculation speed compared to a conventional finite difference simulator (ECLIPSE), a streamline simulator (3DSL) and another streamtube simulator (STUB3D). The simulator developed shows good agreement with other methods for an end-point mobility ratio range from 1 to 50. The hybrid streamtube method (HST) was faster than the updated streamline method (3DSL) by factors of 1 to 3 orders of magnitude, and the conventional finite difference method (ECLIPSE) by factors of more than 3 orders of magnitude. Introduction Streamtubes and streamlines are well known in computational fluid dynamics. In the petroleum industry, numerical computation of Streamtubes was introduced by Higgins and Leighton in the early 1960's. They applied the streamtube technique to two-and three-phase flow in homogeneous, areal systems for several well patterns. They assumed that the geometries of Streamtubes were not changed throughout the displacement process. Under this assumption they used Buckley-Leverett theory6 to calculate the fluid displacement along the Streamtubes. Although the geometries of Streamtubes were fixed throughout the displacement in their work, they showed good agreement with experimental results. Martin and Wegner16 developed a new streamtube method which updates Streamtubes in order to honor the changing mobility field. They compared these updated streamtube results with the fixed streamtube results (Higgins and Leighton method). Their results showed that the fixed streamtube approach is satisfactory for most two-phase problems for mobility ratios ranging from 1 to 1000. Lake et al.14 combined the areal streamtube method with a cross-sectional finite difference method. Their hybrid method assumed that the areal flow is dominated by well placement, whereas the vertical behavior is primarily influenced by geology and the type of displacement. Since Lake et al., this idea has been used extensively.12,5 Thiele21 proposed a new streamtube method which updates streamtube geometries for highly nonlinear displacements in 2-D cross-sections. Since Fay and Prats10, streamline methods have used particle tracking techniques to define streamlines. Shafer19 introduced a Runge-Kutta technique and Pollock17 improved this method by defining a piece-wise linear interpolation of the velocity field within a grid block. Datta-Gupta and King7 developed the same method and introduced the "time-of-flight" concept. Batycky2 used the time-of-flight concept for tracking streamlines and updated their geometries in 3-D models. He showed that his streamline simulator can be applied to large field-scale problems.4,22,3 In 1995, Hewett and Yamada23,11 proposed a theory for the semi-analytical calculation of oil recovery and effective relative permeabilities using fixed streamtube geometries.

  • Fast 3D Reservoir Simulation and Scale Up Using Streamtubes
    Mathematical Geology, 1999
    Co-Authors: Ricardo C. M. Portella, Thomas A. Hewett
    Abstract:

    This paper presents an implementation of a semianalytical method for oil recovery calculation in heterogeneous reservoirs that is both fast and accurate. The method defines streamline paths based on a conventional single-phase incompressible flow calculation. By calculating the time-of-flight for a particle along a streamline and assigning a volumetric flux to each streamline, the cumulative pore volume of a streamtube containing the streamline can be calculated. Subsequently, the streamtube geometries are kept constant and the effects of the time varying mobility distribution in two-phase flow are accounted for by varying the flow rate in each streamtube, based on fluid resistance changes along the streamtube. Oil recovery calculations are then done based on the 1D analytical Buckley–Leverett solution. This concept makes the method extremely fast and easy to implement, making it ideal to simulate large reservoirs generated by geostatiscal methods. The simulation results of a 3D heterogeneous reservoir are presented and compared with those of other simulators. The results shows that the new simulator is much faster than a traditional finite difference simulator, while having the same accuracy. The method also naturally handles the upscaling of absolute and relative permeability. We make use of these upscaling abilities to generate a coarse curvilinear grid that can be used in conventional simulators with a great advantage over conventional upscaled Cartesian grids. This paper also shows an upscaling example using this technique.

  • Upscaling, Gridding, and Simulation Using Streamtubes
    All Days, 1998
    Co-Authors: Ricardo C. M. Portella, Thomas A. Hewett
    Abstract:

    This paper presents an innovative upscaling methodology based on the semi-analytical simulator developed in the first part. The methodology generates a coarse grid based on Streamtubes and isobars, whose upscaled properties are accurately calculated using the properties of each streamtube that constitutes the coarse block. Beyond the calculation of upscaled static properties of the grid, the methodology also calculates upscaled relative permeability curves, or pseudofunctions, using the semi-analytical streamtube method to perform this without requiring any significant additional time. Tests showed that the results from the streamtube coarse grid had an excellent agreement with the fine grid solution. In contrast, simulations with a coarse grid upscaled with conventional techniques failed in many situations. Although this upscaling methodology is heavily based on a fixed streamtube simulation method, it provided good results even for situations in which this streamtube simulator is not supposed to work, such as displacements with favorable mobility ratios, and for problems with gravity and compressibility.

  • Theory for the semi-analytical calculation of oil recovery and effective relative permeabilities using Streamtubes
    Advances in Water Resources, 1997
    Co-Authors: Thomas A. Hewett, Tomomi Yamada
    Abstract:

    Abstract A semi-analytical method has been developed for calculating oil recovery in two and three dimensions, and for calculating effective relative permeabilities for coarse grids. The calculations are based on the assumption that the effects of a changing mobility field can be accounted for by using fixed streamtube geometries with flowrates updated to account for the changing mobility distribution. The single-phase pressure distribution from a numerical solution of Laplace's equation is used to calculate the pressure distribution for a two-phase flow based on a mapping of the solution of the Buckley-Leverett equation onto the Streamtubes derived from the single-phase solution. The displacement calculations for oil recovery are based on theory previously developed by Dykstra and Parsons, extended to include the effects of spatially varying permeability and continuously changing mobilities, as occurs in solutions of the Buckley-Leverett equation for typical values of the mobility ratio. This idea has also been extended to the calculation of effective relative permeabilities for coarse-grid simulation and finally establishes the proper rules for averaging the results of fine-grid numerical simulations of two-phase flow for the definition of effective two-phase flow properties on coarse grids. These calculations have been generalized to three-dimensional flows by the simple device of conceptually inserting a gridded plane across the flow and defining each streamtube at that location as those streamlines which pass through any one of the grid cells. When combined with time-of-flight calculations from the gridded plane to both the producer and injector, the distribution of pore volume along each streamtube can be calculated. This information, combined with a tabulation of the single-phase, steady-state pressure distribution along each streamtube, provides all of the information needed for the semi-analytical calculation of oil recovery and effective flow properties in three-dimensional flows. © 1997 Elsevier Science Ltd. All rights reserved

  • Fast 3-D Reservoir Simulation and Applications Using Streamlines
    All Days, 1997
    Co-Authors: Ricardo C. M. Portella, Thomas A. Hewett
    Abstract:

    Abstract Nowadays there is a great need for flow simulation methods that are at the same time fast and accurate. In this paper we present a streamtube based flow simulation method that is very fast and that can handle large three dimensional reservoir models. The speed of the method relies on the fact that the streamtube geometry is just calculated once. The flow rate of each streamtube is updated based on the total resistance in each streamtube at a given moment. The difficulties of defining Streamtubes in three dimensions are overcome by the use of streamlines and time-of-flight (TOF) techniques. Although the implementation presented here is limited to two-phase, incompressible flow and negligible gravity, it has many direct applications in ranking geostatistical images and history matching techniques. The paper shows several applications using this streamtube simulator. Perhaps the most consequential application of this fast 3-D simulation method is its application in grid generation and upscaling techniques. Introduction The flow simulation of large reservoir models using conventional finite difference simulators is very difficult, and in the majority of the cases not practical without the use of a supercomputer. This situation leads to the use of smaller, coarser grids that usually give poor results in terms of the accuracy of oil production forecasting. So, nowadays many research projects are being conducted to investigate faster methods of flow simulation. The streamtube method is an old technique that recently has received much attention because it provides a fast way to simulate large and complex reservoir models. Streamtube methods basically determine the fluid paths either by solving the stream function equation or by solving the single-phase flow pressure field. Then in each streamtube a one dimensional solution, in the majority of cases the Buckley-Leverett equation solution, is applied to give the final results of the simulation. There are two main approaches in streamtube methods. The first approach considers the Streamtubes fixed in time and the flow rate in each streamtube is updated as the flow proceeds. The second approach considers the flow rate in each streamtube fixed but the position of the Streamtubes is updated as the flow proceeds. A problem that prevented the use of Streamtubes on a larger scale in the past was the extension of the method for three dimensions. The definition of Streamtubes in three dimensions using stream functions is very difficult but the development of particle tracking techniques and the time-of-flight method eliminates this difficulty. In this paper we present a three-dimensional implementation of a streamtube method for oil recovery calculations. This is a fixed streamtube method in which the flow rates are updated according to the total resistance in each streamtube. As we just calculate the streamtube geometries once, the method is very fast and at the same time accurate. Although the method is limited to problems with two-phase, incompressible flow and negligible gravity, it still has many direct applications. Some applications in the ranking of geostatistical images and history matching are shown here. Perhaps the best application of this streamtube method is in the upscaling and grid generation areas. A brief description of the research being conducted in this area is also included in this paper. Semi-analytical Calculation of Oil Recovery All fluids follow paths called streamlines, and this is alo true for flow in porous media. All fluid flow is along the streamlines, that is, there is no flow between two streamlines. In a two dimensional system, two streamlines define a streamtube and narrow Streamtubes can be treatd as a one- dimensional entity so that all the results for one dimensional fluid flow can be applied within it.

David H. Laidlaw - One of the best experts on this subject based on the ideXlab platform.

  • Quantitative Diffusion Tensor Imaging Tractography Metrics are Associated with Cognitive Performance Among HIV-Infected Patients
    Brain Imaging and Behavior, 2010
    Co-Authors: D. F. Tate, Song Zhang, David H. Laidlaw, R. H. Paul, Jared Conley, Kathryn Coop, Wenjin Zhou, Lynn E. Taylor, Timothy Flanigan, Bradford Navia
    Abstract:

    There have been many studies examining HIV-infection-related alterations of magnetic resonance imaging (MRI) diffusion metrics. However, examining scalar diffusion metrics ignores the orientation aspect of diffusion imaging, which can be captured with tractography. We examined five different tractography metrics obtained from global tractography maps (global tractography FA, average tube length, normalized number of Streamtubes, normalized weighted streamtube length, and normalized total number of tubes generated) for differences between HIV positive and negative patients and the association between the metrics and clinical variables of disease severity. We also examined the relationship between these metrics and cognitive performance across a wide range of cognitive domains for the HIV positive and negative patient groups separately. The results demonstrated a significant difference between the groups for global tractography FA ( t  = 2.13, p  = 0.04), but not for any of the other tractography metrics examined ( p -value range = 0.39 to 0.95). There were also several significant associations between the tractography metrics and cognitive performance (i.e., tapping rates, switching 1 and 2, verbal interference, mazes; r  ≥ 0.42) for HIV infected patients. In particular, associations were noted between tractography metrics, speed of processing, fine motor control/speed, and executive function for the HIV-infected patients. These findings suggest that tractography metrics capture clinically relevant information regarding cognitive performance among HIV infected patients and suggests the importance of subtle white matter changes in examining cognitive performance.

  • Visualizing diffusion tensor MR images using Streamtubes and streamsurfaces
    IEEE Transactions on Visualization and Computer Graphics, 2003
    Co-Authors: Song Zhang, Çağatay Demiralp, David H. Laidlaw
    Abstract:

    We present a new method for visualizing 3D volumetric diffusion tensor MR images. We distinguish between linear anisotropy and planar anisotropy and represent values in the two regimes using Streamtubes and streamsurfaces, respectively. Streamtubes represent structures with primarily linear diffusion, typically fiber tracts; streamtube direction correlates with tract orientation. The cross-sectional shape and color of each streamtube represent additional information from the diffusion tensor at each point. Streamsurfaces represent structures in which diffusion is primarily planar. Our algorithm chooses a very small representative subset of the Streamtubes and streamsurfaces for display. We describe the set of metrics used for the culling process, which reduces visual clutter and improves interactivity. We also generate anatomical landmarks to identify the locations of such structures as the eyes, skull surface, and ventricles. The final models are complex surface geometries that can be imported into many interactive graphics software environments. We describe a virtual environment to interact with these models. Expert feedback from doctors studying changes in white-matter structures after gamma-knife capsulotomy and preoperative planning for brain tumor surgery shows that Streamtubes correlate well with major neural structures, the 2D section and geometric landmarks are important in understanding the visualization, and the stereo and interactivity from the virtual environment aid in understanding the complex geometric models.

  • Hierarchical Clustering of Streamtubes
    2002
    Co-Authors: Song Zhang, David H. Laidlaw
    Abstract:

    Introduction We apply hierarchical clustering methods on Streamtubes for visualization and analysis. Streamtubes are integrated in the major eigenvector field of the DTI data set. In a 256 256 50 data set, our algorithm can generate tens of thousands of Streamtubes. It is hard to find features in a dense set of undistinguished tubes. Thus it is important to impose some structural information on the Streamtubes for visualization and interpretation purposes. Hierarchical clustering produces a dendrogram that groups objects into different number of clusters in a continuous way. We apply some clustering methods on a set of Streamtubes and found that the Streamtubes correlating to major neural structures tend to cluster together because of their shape similarities. Also, different distance criteria produce different types of clusters. The dendrogram produced by the hierarchical clustering methods has the potential to be utilized by visualization applications to interactively displa

  • Elucidating Neural Structure in Diffusion Tensor MRI Volumes using Streamtubes and Streamsurfaces
    2001
    Co-Authors: Song Zhang, David H. Laidlaw
    Abstract:

    diffusion tensor MRI images. We distinguish between linear anisotropy and planar anisotropy and represent values within the two regimes using Streamtubes and streamsurfaces, respectively. Streamtubes represent structures with primarily linear diffusion, typically fiber tracts; streamtube direction correlates with tract orientation. The cross-section shape and color of each streamtube are used to represent additional information for the diffusion tensor matrix at each point. Streamsurfaces represent structures in which diffusion is primarily planar. We also generate anatomical landmarks to identify the positions of prominent structures, such as eyes, skull surface, and ventricles. The final models are 2D surface geometries that can be imported into many interactive environments. In the literature, researchers have successfully designed visualization methods for 2D slices of diffusion tensor fields. These include ellipsoids2 as well as a normalized version of the ellipsoids and a painting-motivated method3. Directly extending these methods to volumes would not only be expensive but would also result in selfobscuring geometry. Two approaches have been explored for visualization of 3D second-order tensor fields. One uses volume rendering4, the other uses a geometric representation5. We extend the latter approach, originally applied to tensors related to fluid flow instead of diffusion, to visualize microstructural information in biological tissues. Methods We distinguish between structures exhibiting linear anisotropy and those exhibiting planar anisotropy. Streamtubes and streamsurfaces, respectively, represent these two types of diffusion. Streamtubes represent linear structures, where diffusion is much faster in one direction. The trajectory of each tube sweeps along the principal direction of diffusion, and the cross-section shape is an ellipse representing the diffusion rates in the directions perpendicular to the trajectory. We normalize the maximum radius of the ellipse to a constant value so that the size of the streamtube is predictable while its aspect ratio is preserved. The color of the streamtube shows how anisotropic the diffusion is. Streamsurfaces represent surface structures, where diffusion is faster within a plane than perpendicular to the plane. The surface we generate is an approximation of the integral surface perpendicular to the direction of slowest diffusion. Colors are mapped to the surfaces to show how anisotropic the diffusion is. Our algorithm begins by generating many Streamtubes and streamsurfaces and then culls those down to a representative subset. Initially, every voxel with a linear or planar anisotropy value greater than some threshold has a representative streamtube or a streamsurface. The criteria for selecting the subset to display include the size of the geometry, the average anisotropy in the region containing the geometry, and the similarity of the geometries. Geometries with low scores on these criteria are discarded. A representative subset of geometries is kept and displayed in the final image. Results Figs 1 and 2 illustrate results of our method applied to data acquired from a human brain (data courtesy Dr. Susumu Mori, Johns Hopkins). Many gross features are readily apparent in the results; several are identified in the figures. There are 426 Streamtubes in the final image after the culling process, compared to about 900,000 Streamtubes initially generated. Fig 1. A front view of the human brain image using Streamtubes (red), streamsurfaces (green) and anatomical landmarks (blue ventricles and wireframe brain surface). Anatomical features, including the corpus collosum and corona radiata, are clearly visible in the image.

  • Streamtubes and Streamsurfaces for Visualizing Diffusion Tensor MRI Volume Images
    2000
    Co-Authors: Song Zhang, Charles T. Curry, Daniel S. Morris, David H. Laidlaw
    Abstract:

    resent these two types of diffusion. Streamtubes represent linear structures, where diffusion is much faster in one direction. The trajectory of each tube sweeps along the principal direction of diffusion, and the cross-section shape is an ellipse representing the diffusion rates in the directions perpendicular to the trajectory. We normalize the maximum radius of the ellipse to a constant value so that the size of the streamtube is predictable while its aspect ratio is preserved. The color of the streamtube shows how anisotropic the diffusion is. Streamsurfaces represent surface structures, where diffusion is faster within a plane than perpendicular to the plane. The surface we generate is an approximation of the integral surface perpendicular to the direction of slowest diffusion. Colors are mapped to the surfaces to show how anisotropic the diffusion is. Our algorithm begins by generating many Streamtubes and streamsurfaces and then culls those down to a representative subset. Ini