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Miaomiao Zhang, Ruizhi Liao, Adrian V Dalca, Esra A Turk, Jie Luo, P Ellen Grant, Polina Golland
This paper presents an efficient algorithm for large deformation diffeomorphic metric mapping (LDDMM) with geodesic shooting for image registration. We introduce a novel finite dimensional Fourier representation of diffeomorphic deformations based on the key fact that the high frequency components of a diffeomorphism remain stationary throughout the integration process when computing the deformation associated with smooth velocity fields. We show that manipulating high dimensional diffeomorphisms can be carried out entirely in the bandlimited space by integrating the nonstationary low frequency components of the displacement field...
June 2017: Information Processing in Medical Imaging: Proceedings of the ... Conference
Andreas Mang, Lars Ruthotto
We present an efficient solver for diffeomorphic image registration problems in the framework of Large Deformations Diffeomorphic Metric Mappings (LDDMM). We use an optimal control formulation, in which the velocity field of a hyperbolic PDE needs to be found such that the distance between the final state of the system (the transformed/transported template image) and the observation (the reference image) is minimized. Our solver supports both stationary and non-stationary (i.e., transient or time-dependent) velocity fields...
2017: SIAM Journal on Scientific Computing: a Publication of the Society for Industrial and Applied Mathematics
Monica Hernandez
This paper proposes a method for primal-dual convex optimization in variational large deformation diffeomorphic metric mapping problems formulated with robust regularizers and robust image similarity metrics. The method is based on Chambolle and Pock primal-dual algorithm for solving general convex optimization problems. Diagonal preconditioning is used to ensure the convergence of the algorithm to the global minimum. We consider three robust regularizers liable to provide acceptable results in diffeomorphic registration: Huber, V-Huber and total generalized variation...
November 13, 2017: Physics in Medicine and Biology
Maryam Afzali, Emad Fatemizadeh, Hamid Soltanian-Zadeh
BACKGROUND AND OBJECTIVE: Registration is a critical step in group analysis of diffusion weighted images (DWI). Image registration is also necessary for construction of white matter atlases that can be used to identify white matter changes. A challenge in the registration of DWI is that the orientation of the fiber bundles should be considered in the process, making their registration more challenging than that of the scalar images. Most of the current registration methods use a model of diffusion profile, limiting the method to the used model...
November 2017: Computer Methods and Programs in Biomedicine
Xiao Yang, Roland Kwitt, Martin Styner, Marc Niethammer
This paper introduces Quicksilver, a fast deformable image registration method. Quicksilver registration for image-pairs works by patch-wise prediction of a deformation model based directly on image appearance. A deep encoder-decoder network is used as the prediction model. While the prediction strategy is general, we focus on predictions for the Large Deformation Diffeomorphic Metric Mapping (LDDMM) model. Specifically, we predict the momentum-parameterization of LDDMM, which facilitates a patch-wise prediction strategy while maintaining the theoretical properties of LDDMM, such as guaranteed diffeomorphic mappings for sufficiently strong regularization...
July 11, 2017: NeuroImage
James Fishbaugh, Stanley Durrleman, Marcel Prastawa, Guido Gerig
Many problems in medicine are inherently dynamic processes which include the aspect of change over time, such as childhood development, aging, and disease progression. From medical images, numerous geometric structures can be extracted with various representations, such as landmarks, point clouds, curves, and surfaces. Different sources of geometry may characterize different aspects of the anatomy, such as fiber tracts from DTI and subcortical shapes from structural MRI, and therefore require a modeling scheme which can include various shape representations in any combination...
April 5, 2017: Medical Image Analysis
Karen E Seymour, Xiaoying Tang, Deana Crocetti, Stewart H Mostofsky, Michael I Miller, Keri S Rosch
There has been limited investigation of volume and shape difference in subcortical structures in children with ADHD and a paucity of examination of the influence of sex on these findings. The objective of this study was to examine morphology (volume and shape) of subcortical structures and their association with emotion dysregulation (ED) in girls and boys with ADHD as compared to their typically-developing (TD) counterparts. Participants included 218 children ages 8-12 years old with and without DSM-IV ADHD...
March 30, 2017: Psychiatry Research
Mingzhen Tan, Anqi Qiu
Brain surface registration is an important tool for characterizing cortical anatomical variations and understanding their roles in normal cortical development and psychiatric diseases. However, surface registration remains challenging due to complicated cortical anatomy and its large differences across individuals. In this paper, we propose a fast coarse-to-fine algorithm for surface registration by adapting the large diffeomorphic deformation metric mapping (LDDMM) framework for surface mapping and show improvements in speed and accuracy via a multiresolution analysis of surface meshes and the construction of multiresolution diffeomorphic transformations...
September 2016: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
Mingzhen Tan, Anqi Qiu
Due to the convoluted folding pattern of the cerebral cortex, accurate alignment of cortical surfaces remains challenging. In this paper, we present a multiresolution diffeomorphic surface mapping algorithm under the framework of large deformation diffeomorphic metric mapping (LDDMM). Our algorithm takes advantage of multiresolution analysis (MRA) for surfaces and constructs cortical surfaces at multiresolution. This family of multiresolution surfaces are used as natural sparse priors of the cortical anatomy and provide the anchor points where the parametrization of deformation vector fields is supported...
2015: Information Processing in Medical Imaging: Proceedings of the ... Conference
Miaomiao Zhang, P Thomas Fletcher
This paper presents a fast geodesic shooting algorithm for diffeomorphic image registration. We first introduce a novel finite-dimensional Lie algebra structure on the space of bandlimited velocity fields. We then show that this space can effectively represent initial velocities for diffeomorphic image registration at much lower dimensions than typically used, with little to no loss in registration accuracy. We then leverage the fact that the geodesic evolution equations, as well as the adjoint Jacobi field equations needed for gradient descent methods, can be computed entirely in this finite-dimensional Lie algebra...
2015: Information Processing in Medical Imaging: Proceedings of the ... Conference
Stefan Sommer
We use anisotropic diffusion processes to generalize normal distributions to manifolds and to construct a framework for likelihood estimation of template and covariance structure from manifold valued data. The procedure avoids the linearization that arise when first estimating a mean or template before performing PCA in the tangent space of the mean. We derive flow equations for the most probable paths reaching sampled data points, and we use the paths that are generally not geodesics for estimating the likelihood of the model...
2015: Information Processing in Medical Imaging: Proceedings of the ... Conference
Greg M Fleishman, Boris A Gutman, P Thomas Fletcher, Paul M Thompson
Here we present an algorithm for the simultaneous registration of N longitudinal image pairs such that information acquired by each pair is used to constrain the registration of each other pair. More specifically, in the geodesic shooting setting for Large Deformation Diffeomorphic Metric Mappings (LDDMM) an average of the initial momenta characterizing the N transformations is maintained throughout and updates to individual momenta are constrained to be similar to this average. In this way, the N registrations are coupled and explore the space of diffeomorphisms as a group, the variance of which is constrained to be small...
2015: Information Processing in Medical Imaging: Proceedings of the ... Conference
Jaeil Kim, Maria Del C Valdes-Hernandez, Natalie A Royle, Jinah Park
Accurately recovering the hippocampal shapes against rough and noisy segmentations is as challenging as achieving good anatomical correspondence between the individual shapes. To address these issues, we propose a mesh-to-volume registration approach, characterized by a progressive model deformation. Our model implements flexible weighting scheme for model rigidity under a multi-level neighborhood for vertex connectivity. This method induces a large-to-small scale deformation of a template surface to build the pairwise correspondence by minimizing geometric distortion while robustly restoring the individuals' shape characteristics...
June 2015: IEEE Transactions on Medical Imaging
Dohyung Seo, Ho Jeffrey, Baba C Vemuri
In this paper, we introduce a novel framework for computing a path of diffeomorphisms between a pair of input diffeomorphisms. Direct computation of a geodesic path on the space of diffeomorphisms Diff(Ω) is difficult, and it can be attributed mainly to the infinite dimensionality of Diff(Ω). Our proposed framework, to some degree, bypasses this difficulty using the quotient map of Diff(Ω) to the quotient space Diff(M)/Diff(M) μ obtained by quotienting out the subgroup of volume-preserving diffeomorphisms Diff(M) μ ...
June 2013: Proceedings
François-Xavier Vialard, Laurent Risser
This paper introduces a variational strategy to learn spatially-varying metrics on large groups of images, in the Large Deformation Diffeomorphic Metric Mapping (LDDMM) framework. Spatially-varying metrics we learn not only favor local deformations but also correlated deformations in different image regions and in different directions. In addition, metric parameters can be efficiently estimated using a gradient descent method. We first describe the general strategy and then show how to use it on 3D medical images with reasonable computational ressources...
2014: Medical Image Computing and Computer-assisted Intervention: MICCAI ..
Hock Wei Soon, Anqi Qiu
Whole brain mapping of stroke patients with large cortical infarcts is not trivial due to the complexity of infarcts' anatomical location and appearance in magnetic resonance image. In this study, we proposed an individualized diffeomorphic mapping framework for solving this problem. This framework is based on our recent work of large deformation diffeomorphic metric mapping (LDDMM) in Du et al. (2011) and incorporates anatomical features, such as sulcal/gyral curves, cortical surfaces, brain intensity image, and masks of infarcted regions, in order to align a normal brain to the brain of stroke patients...
January 2015: Magnetic Resonance Imaging
Monica Hernandez
In this work, we propose a novel preconditioned optimization method in the paradigm of Large Deformation Diffeomorphic Metric Mapping (LDDMM). The preconditioned update scheme is formulated for the non-stationary and the stationary parameterizations of diffeomorphisms, yielding three different LDDMM methods. The preconditioning matrices are inspired in the Hessian approximation used in Gauss-Newton method. The derivatives are computed using Frechet differentials. Thus, optimization is performed in a Sobolev space, in contrast to optimization in L(2) commonly used in non-rigid registration literature...
October 21, 2014: Physics in Medicine and Biology
Jia Du, A Pasha Hosseinbor, Moo K Chung, Barbara B Bendlin, Gaurav Suryawanshi, Andrew L Alexander, Anqi Qiu
We first propose a large deformation diffeomorphic metric mapping algorithm to align multiple b-value diffusion weighted imaging (mDWI) data, specifically acquired via hybrid diffusion imaging (HYDI). We denote this algorithm as LDDMM-HYDI. We then propose a Bayesian probabilistic model for estimating the white matter atlas from HYDIs. We adopt the work given in Hosseinbor et al. (2013) and represent the q-space diffusion signal with the Bessel Fourier orientation reconstruction (BFOR) signal basis. The BFOR framework provides the representation of mDWI in the q-space and the analytic form of the emsemble average propagator (EAP) reconstruction, as well as reduces memory requirement...
October 2014: Medical Image Analysis
James Fishbaugh, Marcel Prastawa, Guido Gerig, Stanley Durrleman
Shape regression is emerging as an important tool for the statistical analysis of time dependent shapes. In this paper, we develop a new generative model which describes shape change over time, by extending simple linear regression to the space of shapes represented as currents in the large deformation diffeomorphic metric mapping (LDDMM) framework. By analogy with linear regression, we estimate a baseline shape (intercept) and initial momenta (slope) which fully parameterize the geodesic shape evolution. This is in contrast to previous shape regression methods which assume the baseline shape is fixed...
2013: Information Processing in Medical Imaging: Proceedings of the ... Conference
Jia Du, A Pasha Hosseinbor, Moo K Chung, Barbara B Bendlin, Gaurav Suryawanshi, Gaurav Suryawanshi, Anqi Qiu
In this paper, we propose a large deformation diffeomorphic metric mapping algorithm to align multiple b-value diffusion weighted imaging (mDWI) data, specifically acquired via hybrid diffusion imaging (HYDI), denoted as LDDMM-HYDI. We adopt the work given in Hosseinbor et al. (2012) and represent the q-space diffusion signal with the Bessel Fourier orientation reconstruction (BFOR) signal basis. The BFOR framework provides the representation of mDWI in the q-space and thus reduces memory requirement. In addition, since the BFOR signal basis is orthonormal, the L2 norm that quantifies the differences in q-space signals of any two mDWI datasets can be easily computed as the sum of the squared differences in the BFOR expansion coefficients...
2013: Information Processing in Medical Imaging: Proceedings of the ... Conference
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