multigrid acceleration for recirculating laminar and turbulent flows computed with a non orthogonal collocated finite volume scheme abstract a study has been undertaken of multigrid convergence acceleration in iterative calculations of recirculating laminar and turbulent flows the basic numerical platform is a 2d 3d non orthogonal collocated finite volume algorithm in which convection is approximated optionally by a non monotonic upstream weighted third order scheme or by a monotonie second order muscl tvd formulation and which iterates the solution towards the steady state by way of a pressure correction scheme the study investigates the performance of various multigrid implementations including the correction and full approximation multigrid variants the latter operated within a variety of cycles both with prescribed and residual driven relaxation sweeps at each grid level the multigrid implementation is documented in detail and includes a consideration of data structure issues and special algorithmic measures necessary to secure robust convergence for turbulent flows the performance characteristics of the multigrid variants are then exposed through a range of results arising from computations for laminar and turbulent conditions with turbulence being represented by the k model or full reynolds stress transport closure

applying tensor based morphometry to parametric surfaces can improve mri based disease diagnosis many methods have been proposed for computer assisted diagnostic classification full tensor information and machine learning with 3d maps derived from brain images may help detect subtle differences or classify subjects into different groups here we develop a new approach to apply tensor based morphometry to parametric surface models for diagnostic classification we use this approach to identify cortical surface features for use in diagnostic classifiers first with holomorphic 1 forms we compute an efficient and accurate conformal mapping from a multiply connected mesh to the so called slit domain next the surface parameterization approach provides a natural way to register anatomical surfaces across subjects using a constrained harmonic map to analyze anatomical differences we then analyze the full riemannian surface metric tensors which retain multivariate information on local surface geometry as the number of voxels in a 3d image is large sparse learning is a promising method to select a subset of imaging features and to improve classification accuracy focusing on vertices with greatest effect sizes we train a diagnostic classifier using the surface features selected by an l1 norm based sparse learning method stability selection is applied to validate the selected feature sets we tested the algorithm on mri derived cortical surfaces from 42 subjects with genetically confirmed williams syndrome and 40 age matched controls multivariate statistics on the local tensors gave greater effect sizes for detecting group differences relative to other tbm based statistics including analysis of the jacobian determinant and the largest eigenvalue of the surface metric our method also gave reasonable classification results relative to the jacobian determinant the pair of eigenvalues of the jacobian matrix and volume features this analysis pipeline may boost the power of morphometry studies and may assist with image based classification

review of shape representation and description techniques more and more images have been generated in digital form around the world there is a growing interest in 1nding images in large collections or from remote databases in order to 1nd an image the image has to be described or represented by certain features shape is an important visual feature of an image searching for images using shape features has attracted much attention there are many shape representation anddescription techniques in the literature in this paper we classify and review these important techniques we examine implementation procedures for each technique and discuss its advantages and disadvantages some recent research results are also included and discussed in this paper finally we identify some promising techniques for image retrieval according to standard principles

brain structural mapping using a novel hybrid implicit explicit framework based on the level set method this paper presents a novel approach to feature based brain image warping by using a hybrid implicit explicit framework which unifies many prior approaches in a common framework in the first step we develop links between image warping and the level set method and we formulate the fundamental mathematics required for this hybrid implicit explicit approach in the second step we incorporate the large deformation models into these formulations leading to a complete and elegant treatment of anatomical structure matching in this latest approach exact matching of anatomy is achieved by comparing the target to the warped source structure under the forward mapping and the source to the warped target structure under the backward mapping because anatomy is represented nonparametrically a path is constructed linking the source to the target structure without prior knowledge of their point correspondence the final point correspondence is constructed based on the linking path with the minimal energy intensity similarity measures can be naturally incorporated in the same framework as landmark constraints by combining them in the gradient descent body forces we illustrate the approach with two applications 1 tensor based morphometry of the corpus callosum in autistic children and 2 matching cortical surfaces to measure the profile of cortical anatomic variation in summary the new mathematical techniques introduced here contribute fundamentally to the mapping of brain structure and its variation and provide a framework that unites feature and intensity based image registration techniques

hammer hierarchical attribute matching mechanism for elastic registration a new approach is presented for elastic registration of medical images and is applied to magnetic resonance images of the brain experimental results demonstrate very high accuracy in superposition of images from different subjects there are two major novelties in the proposed algorithm first it uses an attribute vector i e a set of geometric moment invariants gmis that are defined on each voxel in an image and are calculated from the tissue maps to reflect the underlying anatomy at different scales the attribute vector if rich enough can distinguish between different parts of an image which helps establish anatomical correspondences in the deformation procedure it also helps reduce local minima by reducing ambiguity in potential matches this is a fundamental deviation of our method referred to as the hierarchical attribute matching mechanism for elastic registration hammer from other volumetric deformation methods which are typically based on maximizing image similarity second in order to avoid being trapped by local minima i e suboptimal poor matches hammer uses a successive approximation of the energy function being optimized by lower dimensional smooth energy functions which are constructed to have significantly fewer local minima this is achieved by hierarchically selecting the driving features that have distinct attribute vectors thus drastically reducing ambiguity in finding correspondence a number of experiments demonstrate that the proposed algorithm results in accurate superposition of image data from individuals with significant anatomical differences

the detection of local shape changes via the geometry of hotelling s t 2 fields this paper is motivated by the problem of detecting local changes or differences in shape between two samples of objects via the nonlinear deformations required to map each object to an atlas standard local shape changes are then detected by high values of the random field of hotelling s t 2 statistics for detecting a change in mean of the vector deformations at each point in the object to control the null probability of detecting a local shape change we use the recent result of adler that the probability that a random field crosses a high threshold is very accurately approximated by the expected euler characteristic ec of the excursion set of the random field above the threshold we give an exact expression for the expected ec of a hotelling s t 2 field and we study the behavior of the field near local extrema this extends previous results for gaussian random fields by adler and x 2 t and f fields by worsley and cao for illustration these results are applied to the detection of differences in brain shape between a sample of 29 males and 23 females

consistent image registration presents a new method for image registration based on jointly estimating the forward and reverse transformations between two images while constraining these transforms to be inverses of one another this approach produces a consistent set of transformations that have less pairwise registration error i e better correspondence than traditional methods that estimate the forward and reverse transformations independently the transformations are estimated iteratively and are restricted to preserve topology by constraining them to obey the laws of continuum mechanics the transformations are parameterized by a fourier series to diagonalize the covariance structure imposed by the continuum mechanics constraints and to provide a computationally efficient numerical implementation results using a linear elastic material constraint are presented using both magnetic resonance and x ray computed tomography image data the results show that the joint estimation of a consistent set of forward and reverse transformations constrained by linear elasticity give better registration results than using either constraint alone or none at all

brain surface conformal parameterization with the ricci flow in brain mapping research parameterized 3 d surface models are of great interest for statistical comparisons of anatomy surface based registration and signal processing here we introduce the theories of continuous and discrete surface ricci flow which can create riemannian metrics on surfaces with arbitrary topologies with user defined gaussian curvatures the resulting conformal parameterizations have no singularities and they are intrinsic and stable first we convert a cortical surface model into a multiple boundary surface by cutting along selected anatomical landmark curves secondly we conformally parameterize each cortical surface to a parameter domain with a user designed gaussian curvature arrangement in the parameter domain a shape index based on conformal invariants is computed and inter subject cortical surface matching is performed by solving a constrained harmonic map we illustrate various target curvature arrangements and demonstrate the stability of the method using longitudinal data to map statistical differences in cortical morphometry we studied brain asymmetry in 14 healthy control subjects we used a manifold version of hotelling s t2 test applied to the jacobian matrices of the surface parameterizations a permutation test along with the cumulative distribution of p values were used to estimate the overall statistical significance of differences the results show our algorithm s power to detect subtle group differences in cortical surfaces

tensor based cortical surface morphometry via weighted spherical harmonic representation we present a new tensor based morphometric framework that quantifies cortical shape variations using a local area element the local area element is computed from the riemannian metric tensors which are obtained from the smooth functional parametrization of a cortical mesh for the smooth parametrization we have developed a novel weighted spherical harmonic spharm representation which generalizes the traditional spharm as a special case for a specific choice of weights the weighted spharm is shown to be the least squares approximation to the solution of an isotropic heat diffusion on a unit sphere the main aims of this paper are to present the weighted spharm and to show how it can be used in the tensor based morphometry as an illustration the methodology has been applied in the problem of detecting abnormal cortical regions in the group of high functioning autistic subjects

exit problem and control theory abstract the first part of the paper is concerned with a version of freidlin wentzell exit theorems suitable for control theoretic applications in the second part the general results are specialized to the case of linear systems and two types of stabilizability questions are considered

near isometric flattening of brain surfaces flattened representations of brain surfaces are often used to visualize and analyze spatial patterns of structural organization and functional activity here we present a set of rigorous criteria and accompanying test cases with which to evaluate flattening algorithms that attempt to preserve shortest path distances on the original surface we also introduce a novel flattening algorithm that is the first to satisfy all of these criteria and demonstrate its ability to produce accurate flat maps of human and macaque visual cortex using this algorithm we have recently obtained results showing a remarkable unexpected degree of consistency in the shape and topographic structure of visual cortical areas within humans and macaques as well as between these two species

a multi resolution scheme for distortion minimizing mapping between human subcortical structures based on geodesic construction on riemannian manifolds in this paper we deal with a subcortical surface registration problem subcortical structures including hippocampi and caudates have a small number of salient features such as heads and tails unlike cortical surfaces therefore it is hard if not impossible to perform subcortical surface registration with only such features it is also non trivial for neuroanatomical experts to select landmarks consistently for subcortical surfaces of different subjects we therefore present a landmark free approach for subcortical surface registration by measuring the amount of mesh distortion between subcortical surfaces assuming that the surfaces are represented by meshes the input meshes can be constructed using any surface modeling tool available in the public domain since our registration method is independent of a surface modeling process given the source and target surfaces together with their representing meshes the vertex positions of the source mesh are iteratively displaced while preserving the underlying surface shape in order to minimize the distortion to the target mesh by representing each surface mesh as a point on a high dimensional riemannian manifold we define a distance metric on the manifold that measures the amount of distortion from a given source mesh to the target mesh based on the notion of isometry while penalizing triangle flipping under this metric we reduce the distortion minimization problem to the problem of constructing a geodesic curve from the moving source point to the fixed target point on the manifold while satisfying the shape preserving constraint we adopt a multi resolution framework to solve the problem for distortion minimizing mapping between the source and target meshes we validate our registration scheme through several experiments distance metric comparison visual validation using real data robustness test to mesh variations feature alignment using anatomic landmarks consistency with previous clinical findings and comparison with a surface based registration method lddmm surface

deformable templates using large deformation kinematics a general automatic approach is presented for accommodating local shape variation when mapping a two dimensional 2 d or three dimensional 3 d template image into alignment with a topologically similar target image local shape variability is accommodated by applying a vector field transformation to the underlying material coordinate system of the template while constraining the transformation to be smooth globally positive definite jacobian smoothness is guaranteed without specifically penalizing large magnitude deformations of small subvolumes by constraining the transformation on the basis of a stokesian limit of the fluid dynamical navier stokes equations this differs fundamentally from quadratic penalty methods such as those based on linearized elasticity or thin plate splines in that stress restraining the motion relaxes over time allowing large magnitude deformations kinematic nonlinearities are inherently necessary to maintain continuity of structures during large magnitude deformations and are included in all results after initial global registration final mappings are obtained by numerically solving a set of nonlinear partial differential equations associated with the constrained optimization problem automatic regridding is performed by propagating templates as the nonlinear transformations evaluated on a finite lattice become singular application of the method to intersubject registration of neuroanatomical structures illustrates the ability to account for local anatomical variability

continuous medial representation of brain structures using the biharmonic pde a new approach for constructing deformable continuous medial models for anatomical structures is presented medial models describe geometrical objects by first specifying the skeleton of the object and then deriving the boundary surface corresponding to the skeleton however an arbitrary specification of a skeleton will not be valid unless a certain set of sufficient conditions is satisfied the most challenging of these is the non linear equality constraint that must hold along the boundaries of the manifolds forming the skeleton the main contribution of this paper is to leverage the biharmonic partial differential equation as a mapping from a codimension 0 subset of euclidean space to the space of skeletons that satisfy the equality constraint the pde supports robust numerical solution on freeform triangular meshes providing additional flexibility for shape modeling the approach is evaluated by generating continuous medial models for a large dataset of hippocampus shapes generalizations to modeling more complex shapes and to representing branching skeletons are demonstrated

diffeomorphic metric surface mapping in subregion of the superior temporal gyrus this paper describes the application of large deformation diffeomorphic metric mapping to cortical surfaces based on the shape and geometric properties of subregions of the superior temporal gyrus in the human brain the anatomical surfaces of the cortex are represented as triangulated meshes the diffeomorphic matching algorithm is implemented by defining a norm between the triangulated meshes based on the algorithms of vaillant and glaunes the diffeomorphic correspondence is defined as a flow of the extrinsic three dimensional coordinates containing the cortical surface that registers the initial and target geometry by minimizing the norm the methods are demonstrated in 40 high resolution mri cortical surfaces of planum temporale pt constructed from subsets of the superior temporal gyrus stg the effectiveness of the algorithm is demonstrated via the euclidean positional distance distance of normal vectors and curvature before and after the surface matching as well as the comparison with a landmark matching algorithm the results demonstrate that both the positional and shape variability of the anatomical configurations are being represented by the diffeomorphic maps

multi manifold diffeomorphic metric mapping for aligning cortical hemispheric surfaces cortical surface based analysis has been widely used in anatomical and functional studies because it is geometrically appropriate for the cortex one of the main challenges in the cortical surface based analysis is to optimize the alignment of the cortical hemispheric surfaces across individuals in this paper we introduce a multi manifold large deformation diffeomorphic metric mapping mm lddmm algorithm that allows simultaneously carrying the cortical hemispheric surface and its sulcal curves from one to the other through a flow of diffeomorphisms we present an algorithm based on recent derivation of a law of momentum conservation for the geodesics of diffeomorphic flow once a template is fixed the space of initial momentum becomes an appropriate space for studying shape via geodesic flow since the flow at any point on curves and surfaces along the geodesic is completely determined by the momentum at the origin we solve for trajectories geodesics of the kinetic energy by computing its variation with respect to the initial momentum and by applying a gradient descent scheme the mm lddmm algorithm optimizes the initial momenta encoding the anatomical variation of each individual relative to a common coordinate system in a linear space which provides a natural scheme for shape deformation average and template or atlas generation we applied the mm lddmm algorithm for constructing the templates for the cortical surface and 14 sulcal curves of each hemisphere using a group of 40 subjects the estimated template shape reflects regions which are highly variable across these subjects compared with existing single manifold lddmm algorithms such as the lddmm curve mapping and the lddmm surface mapping the mm lddmm mapping provides better results in terms of surface to surface distances in five predefined regions

surface fluid registration of conformal representation application to detect disease burden and genetic influence on hippocampus in this paper we develop a new automated surface registration system based on surface conformal parameterization by holomorphic 1 forms inverse consistent surface fluid registration and multivariate tensor based morphometry mtbm first we conformally map a surface onto a planar rectangle space with holomorphic 1 forms second we compute surface conformal representation by combining its local conformal factor and mean curvature and linearly scale the dynamic range of the conformal representation to form the feature image of the surface third we align the feature image with a chosen template image via the fluid image registration algorithm which has been extended into the curvilinear coordinates to adjust for the distortion introduced by surface parameterization the inverse consistent image registration algorithm is also incorporated in the system to jointly estimate the forward and inverse transformations between the study and template images this alignment induces a corresponding deformation on the surface we tested the system on alzheimer s disease neuroimaging initiative adni baseline dataset to study ad symptoms on hippocampus in our system by modeling a hippocampus as a 3d parametric surface we nonlinearly registered each surface with a selected template surface then we used mtbm to analyze the morphometry difference between diagnostic groups experimental results show that the new system has better performance than two publicly available subcortical surface registration tools first and spharm we also analyzed the genetic influence of the apolipoprotein e 4 allele apoe4 which is considered as the most prevalent risk factor for ad our work successfully detected statistically significant difference between apoe4 carriers and non carriers in both patients of mild cognitive impairment mci and healthy control subjects the results show evidence that the apoe genotype may be associated with accelerated brain atrophy so that our work provides a new mri analysis tool that may help presymptomatic ad research

a bayesian model of shape and appearance for subcortical brain segmentation automatic segmentation of subcortical structures in human brain mr images is an important but difficult task due to poor and variable intensity contrast clear well defined intensity features are absent in many places along typical structure boundaries and so extra information is required to achieve successful segmentation a method is proposed here that uses manually labelled image data to provide anatomical training information it utilises the principles of the active shape and appearance models but places them within a bayesian framework allowing probabilistic relationships between shape and intensity to be fully exploited the model is trained for 15 different subcortical structures using 336 manually labelled t1 weighted mr images using the bayesian approach conditional probabilities can be calculated easily and efficiently avoiding technical problems of ill conditioned covariance matrices even with weak priors and eliminating the need for fitting extra empirical scaling parameters as is required in standard active appearance models furthermore differences in boundary vertex locations provide a direct purely local measure of geometric change in structure between groups that unlike voxel based morphometry is not dependent on tissue classification methods or arbitrary smoothing in this paper the fully automated segmentation method is presented and assessed both quantitatively using leave one out testing on the 336 training images and qualitatively using an independent clinical dataset involving alzheimer s disease median dice overlaps between 0 7 and 0 9 are obtained with this method which is comparable or better than other automated methods an implementation of this method called first is currently distributed with the freely available fsl package

controlling the false discovery rate a practical and powerful approach to multiple testing summary the common approach to the multiplicity problem calls for controlling the familywise error rate fwer this approach though has faults and we point out a few a different approach to problems of multiple significance testing is presented it calls for controlling the expected proportion of falsely rejected hypotheses the false discovery rate this error rate is equivalent to the fwer when all hypotheses are true but is smaller otherwise therefore in problems where the control of the false discovery rate rather than that of the fwer is desired there is potential for a gain in power a simple sequential bonferronitype procedure is proved to control the false discovery rate for independent test statistics and a simulation study shows that the gain in power is substantial the use of the new procedure and the appropriateness of the criterion are illustrated with examples

variational methods for multimodal image matching matching images of different modalities can be achieved by the maximization of suitable statistical similarity measures within a given class of geometric transformations handling complex nonrigid deformations in this context turns out to be particularly difficult and has attracted much attention in the last few years the thrust of this paper is that many of the existing methods for nonrigid monomodal registration that use simple criteria for comparing the intensities e g ssd can be extended to the multimodal case where more complex intensity similarity measures are necessary to this end we perform a formal computation of the variational gradient of a hierarchy of statistical similarity measures and use the results to generalize a recently proposed and very effective optical flow algorithm l alvarez j weickert and j sanchez 2000 technical report and ijcv 39 1 41 56 to the case of multimodal image registration our method readily extends to the case of locally computed similarity measures thus providing the flexibility to cope with spatial non stationarities in the way the intensities in the two images are related the well posedness of the resulting equations is proved in a complementary work o d faugeras and g hermosillo 2001 technical report 4235 inria using well established techniques in functional analysis we briefly describe our numerical implementation of these equations and show results on real and synthetic data