Ensemble tractography

Fiber tractography uses diffusion MRI to estimate the trajectory and cortical projection zones of white matter fascicles in the living human brain. There are many different tractography algorithms and each requires the user to set several parameters, such as curvature threshold. Choosing a single algorithm with a specific parameters sets poses two challenges. First, different algorithms and parameter values produce different results. Second, the optimal choice of algorithm and parameter value may differ between different white matter regions or different fascicles, subjects, and acquisition parameters. We propose using ensemble methods to reduce algorithm and parameter dependencies. To do so we separate the processes of fascicle generation and evaluation. Specifically, we analyze the value of creating optimized connectomes by systematically combining candidate fascicles from an ensemble of algorithms (deterministic and probabilistic) and sweeping through key parameters (curvature and stopping criterion). The ensemble approach leads to optimized connectomes that provide better cross-validatedprediction error of the diffusion MRI data than optimized connectomes generated using the singlealgorithms or parameter set. Furthermore, the ensemble approach produces connectomes that contain both short- and long-range fascicles, whereas single-parameter connectomes are biased towards one or the other. In summary, a systematic ensemble tractography approach can produce connectomes that are superior to standard single parameter estimates both for predicting the diffusion measurements and estimating white matter fascicles.Fil: Takemura, Hiromasa. University of Stanford; Estados Unidos. Osaka University; JapónFil: Caiafa, César Federico. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Instituto Argentino de Radioastronomía. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Argentino de Radioastronomía; ArgentinaFil: Wandell, Brian A.. University of Stanford; Estados UnidosFil: Pestilli, Franco. Indiana University; Estados Unido

Modeling single-phase flow and solute transport across scales

textFlow and transport phenomena in the subsurface often span a wide range of length (nanometers to kilometers) and time (nanoseconds to years) scales, and frequently arise in applications of CO₂ sequestration, pollutant transport, and near-well acid stimulation. Reliable field-scale predictions depend on our predictive capacity at each individual scale as well as our ability to accurately propagate information across scales. Pore-scale modeling (coupled with experiments) has assumed an important role in improving our fundamental understanding at the small scale, and is frequently used to inform/guide modeling efforts at larger scales. Among the various methods, there often exists a trade-off between computational efficiency/simplicity and accuracy. While high-resolution methods are very accurate, they are computationally limited to relatively small domains. Since macroscopic properties of a porous medium are statistically representative only when sample sizes are sufficiently large, simple and efficient pore-scale methods are more attractive. In this work, two Eulerian pore-network models for simulating single-phase flow and solute transport are developed. The models focus on capturing two key pore-level mechanisms: a) partial mixing within pores (large void volumes), and b) shear dispersion within throats (narrow constrictions connecting the pores), which are shown to have a substantial impact on transverse and longitudinal dispersion coefficients at the macro scale. The models are verified with high-resolution pore-scale methods and validated against micromodel experiments as well as experimental data from the literature. Studies regarding the significance of different pore-level mixing assumptions (perfect mixing vs. partial mixing) in disordered media, as well as the predictive capacity of network modeling as a whole for ordered media are conducted. A mortar domain decomposition framework is additionally developed, under which efficient and accurate simulations on even larger and highly heterogeneous pore-scale domains are feasible. The mortar methods are verified and parallel scalability is demonstrated. It is shown that they can be used as “hybrid” methods for coupling localized pore-scale inclusions to a surrounding continuum (when insufficient scale separation exists). The framework further permits multi-model simulations within the same computational domain. An application of the methods studying “emergent” behavior during calcite precipitation in the context of geologic CO₂ sequestration is provided.Petroleum and Geosystems Engineerin

Some experiences with the viscous-inviscid interaction approach

Methods for simulating compressible viscous flow using the viscid-inviscid interaction approach are described. The formulations presented range from the more familiar full-potential/boundary-layer interaction schemes to a method for coupling Euler/Navier-Stokes and boundary-layer algorithms. An effort is made to describe the advantages and disadvantages of each formulation. Sample results are presented which illustrate the applicability of the methods

The functional anatomy of white matter pathways for visual configuration learning

The role of the medial temporal lobes (MTL) in visuo-spatial learning has been extensively studied and documented in the neuroscientific literature. Numerous animal and human studies have demonstrated that the parahippocampal place area (PPA), which sits at the confluence of the parahippocampal and lingual gyri, is particularly important for learning the spatial configuration of objects in visually presented scenes. In current visuo-spatial processing models, the PPA sits downstream from the parietal lobes which are involved in multiple facets of spatial processing. Yet, direct input to the PPA from early visual cortex (EVC) is rarely discussed and poorly understood. This thesis adopted a multimodal neuroimaging analysis approach to study the functional anatomy of these connections. First, the pattern of structural connectivity between EVC and the MTL was explored by means of surface-based ‘connectomes’ constructed from diffusion MRI tractography in a cohort of 200 healthy young adults from the Human Connectome Project. Through this analysis, the PPA emerged as a primary recipient of EVC connections within the MTL. Second, a data-driven clustering analysis of the PPA’s connectivity to an extended cortical region (including EVC, retrosplenial cortex, and other areas) revealed multiple clusters with different connectivity profiles within the PPA. The two main clusters were located in the posterior and anterior portions of the PPA, with the posterior cluster preferentially connected to EVC. Motivated by this result, virtual tractography dissections were used to delineate the medial occipital longitudinal tract (MOLT), the white matter bundle connecting the PPA with EVC. The properties of this bundle and its relation to visual configuration learning were verified in a different, cross-sectional adult cohort of 90 subjects. Finally, the role of the MOLT in the visuo-spatial learning domain was further confirmed in the case of a stroke patient who, after bilateral occipital injury, exhibited deficits confined to this domain. The results presented in this work suggest that the MOLT should be included in current visuo-spatial processing models as it offers additional insight into how the MTL acquires and processes information for spatial learning

Analyse et reconstruction de faisceaux de la matière blanche

L'imagerie par résonance magnétique de diffusion (IRMd) est une modalité d'acquisition permettant de sonder les tissus biologiques et d'en extraire une variété d'informations sur le mouvement microscopique des molécules d'eau. Plus spécifiquement à l'imagerie médicale, l'IRMd permet l'investigation des structures fibreuses de nombreux organes et facilite la compréhension des processus cognitifs ou au diagnostic. Dans le domaine des neurosciences, l'IRMd est cruciale à l'exploration de la connectivité structurelle de la matière blanche. Cette thèse s'intéresse plus particulièrement à la reconstruction de faisceaux de la matière blanche ainsi qu'à leur analyse. Toute la complexité du traitement des données commençant au scanneur jusqu'à la création d'un tractogramme est extrêmement importante. Par contre, l'application spécifique de reconstruction des faisceaux anatomiques plausibles est ultimement le véritable défi de l'IRMd. L'optimisation des paramètres de la tractographie, le processus de segmentation manuelle ou automatique ainsi que l'interprétation des résultats liée à ces faisceaux sont toutes des étapes du processus avec leurs lots de difficultés

Resource management for data streaming applications

This dissertation investigates novel middleware mechanisms for building streaming applications. Developing streaming applications is a challenging task because (i) they are continuous in nature; (ii) they require fusion of data coming from multiple sources to derive higher level information; (iii) they require efficient transport of data from/to distributed sources and sinks; (iv) they need access to heterogeneous resources spanning sensor networks and high performance computing; and (v) they are time critical in nature. My thesis is that an intuitive programming abstraction will make it easier to build dynamic, distributed, and ubiquitous data streaming applications. Moreover, such an abstraction will enable an efficient allocation of shared and heterogeneous computational resources thereby making it easier for domain experts to build these applications. In support of the thesis, I present a novel programming abstraction, called DFuse, that makes it easier to develop these applications. A domain expert only needs to specify the input and output connections to fusion channels, and the fusion functions. The subsystems developed in this dissertation take care of instantiating the application, allocating resources for the application (via the scheduling heuristic developed in this dissertation) and dynamically managing the resources (via the dynamic scheduling algorithm presented in this dissertation). Through extensive performance evaluation, I demonstrate that the resources are allocated efficiently to optimize the throughput and latency constraints of an application.Ph.D.Committee Chair: Ramachandran, Umakishore; Committee Member: Chervenak, Ann; Committee Member: Cooper, Brian; Committee Member: Liu, Ling; Committee Member: Schwan, Karste

Stream bundles - cohesive advection through flow fields

Journal ArticleStreamline advection has proven an effective method for visualizing vector flow field data. Traditional streamlines do not, however, provide for investigating the coarsergrained features of complex datasets, such as the white matter tracts in the brain or the thermal conveyor belts in the ocean. In this paper, we introduce a cohesive advection primitive, called a stream bundle. Whereas traditional streamlines describe the advection patterns of single, infinitesimal micro-particles, stream bundles indicate advection paths for large macro-particles. Implementationally, stream bundles are composed of a collection of individual streamlines (here termed fibers), each of which only advects a short distance before being terminated and re-seeded in a new location. The individual fibers combine to dictate the instantaneous distribution of the bundle, and it is this collective distribution which is used in determining where fibers are reseeded. By carefully controlling the termination and re-seeding policies of the fibers, we can prevent the bundle from becoming frayed in divergent regions. By maintaining a cohesive from, the bundles can indicate the coarse structure of complex vector fields. In this paper, we use stream bundles to investigate the oceanic currents