We propose numerical algorithms for solving large deformation diffeomorphic image registration problems. We formulate the nonrigid image registration problem as a problem of optimal control. This leads to an infinite-dimensional partial differential equation (PDE) constrained optimization problem.
The PDE constraint consists, in its simplest form, of a hyperbolic transport equation for the evolution of the image intensity. The control variable is the velocity field. Tikhonov regularization on the control ensures well-posedness. We consider standard smoothness regularization based on $H^1$- or $H^2$-seminorms. We augment this regularization scheme with a constraint on the divergence of the velocity field rendering the deformation incompressible and thus ensuring that the determinant of the deformation gradient is equal to one, up to the numerical error.
We use a Fourier pseudospectral discretization in space and a Chebyshev pseudospectral discretization in time. We use a preconditioned, globalized, matrix-free, inexact Newton-Krylov method for numerical optimization. A parameter continuation is designed to estimate an optimal regularization parameter. Regularity is ensured by controlling the geometric properties of the deformation field. Overall, we arrive at a black-box solver. We study spectral properties of the Hessian, grid convergence, numerical accuracy, computational efficiency, and deformation regularity of our scheme. We compare the designed Newton-Krylov methods with a globalized preconditioned gradient descent. We study the influence of a varying number of unknowns in time.
The reported results demonstrate excellent numerical accuracy, guaranteed local deformation regularity, and computational efficiency with an optional control on local mass conservation. The Newton-Krylov methods clearly outperform the Picard method if high accuracy of the inversion is required.
The Institute for Computational Engineering and Sciences, The University of Texas at Austin（得克萨斯大学奥斯汀分校计算工程与科学研究所）；Department of Mathematics at the University of Houston（休斯顿大学数学系）
We propose an efficient numerical algorithm for the solution of diffeomorphic image registration problems. We use a variational formulation constrained by a partial differential equation (PDE), where the constraints are a scalar transport equation. We use a pseudospectral discretization in space and second-order accurate semi-Lagrangian time stepping scheme for the transport equations. We solve for a stationary velocity field using a preconditioned, globalized, matrix-free Newton-Krylov scheme. We propose and test a two-level Hessian preconditioner. We consider two strategies for inverting the…
Institute for Computational Engineering and Sciences, University of Texas at Austin（德克萨斯大学奥斯汀分校计算工程与科学研究所）；Department of Mathematics and Computer Science, Emory University（埃默里大学数学与计算机科学系）
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. As transformation models, we consider both the transport equation (ass…
University of Houston（休斯顿大学）；University of California, Berkeley（加州大学伯克利分校）；University of Pennsylvania（宾夕法尼亚大学）；University of Texas at Austin（德克萨斯大学奥斯汀分校）
With this work, we release CLAIRE, a distributed-memory implementation of an effective solver for constrained large deformation diffeomorphic image registration problems in three dimensions. We consider an optimal control formulation. We invert for a stationary velocity field that parameterizes the deformation map. Our solver is based on a globalized, preconditioned, inexact reduced space Gauss--Newton--Krylov scheme. We exploit state-of-the-art techniques in scientific computing to develop an effective solver that scales to thousands of distributed memory nodes on high-end clusters. We presen…
This paper is concerned with the regularization of large-scale discrete inverse problems by means of inexact Krylov methods. Specifically, we derive two new inexact Krylov methods that can be efficiently applied to unregularized or Tikhonov-regularized least squares problems, and we study their theoretical properties, including links with their exact counterparts and strategies to monitor the amount of inexactness. We then apply the new methods to separable nonlinear inverse problems arising in blind deblurring. In this setting inexactness stems from the uncertainty in the parameters defining …
In this work, we address the implementation and performance of inexact Newton-Krylov and quasi-Newton algorithms, more specifically the BFGS method, for the solution of the nonlinear elasticity equations, and compare them to a standard Newton-Krylov method. This is done through a systematic analysis of the performance of the solvers with respect to the problem size, the magnitude of the data and the number of processors in both almost incompressible and incompressible mechanics. We consider three test cases: Cook's membrane (static, almost incompressible), a twist test (static, incompressible)…
The Institute for Computational Engineering and Sciences, The University of Texas at Austin（德克萨斯大学奥斯汀分校计算工程与科学研究所）
We propose regularization schemes for deformable registration and efficient algorithms for their numerical approximation. We treat image registration as a variational optimal control problem. The deformation map is parametrized by its velocity. Tikhonov regularization ensures well-posedness. Our scheme augments standard smoothness regularization operators based on $H^1$- and $H^2$-seminorms with a constraint on the divergence of the velocity field, which resembles variational formulations for Stokes incompressible flows. In our formulation, we invert for a stationary velocity field and a mass …
The FEAST eigenvalue algorithm is a subspace iteration algorithm that uses contour integration in the complex plane to obtain the eigenvectors of a matrix for the eigenvalues that are located in any user-defined search interval. By computing small numbers of eigenvalues in specific regions of the complex plane, FEAST is able to naturally parallelize the solution of eigenvalue problems by solving for multiple eigenpairs simultaneously. The traditional FEAST algorithm is implemented by directly solving collections of shifted linear systems of equations; in this paper, we describe a variation of …
We present a parallel distributed-memory algorithm for large deformation diffeomorphic registration of volumetric images that produces large isochoric deformations (locally volume preserving). Image registration is a key technology in medical image analysis. Our algorithm uses a partial differential equation constrained optimal control formulation. Finding the optimal deformation map requires the solution of a highly nonlinear problem that involves pseudo-differential operators, biharmonic operators, and pure advection operators both forward and back- ward in time. A key issue is the time to s…
Matrix exponential discriminant analysis (EDA) is a generalized discriminant analysis method based on matrix exponential. It can essentially overcome the intrinsic difficulty of small sample size problem that exists in the classical linear discriminant analysis (LDA). However, for data with high dimension, one has to solve a large matrix exponential eigenproblem in this method, and the time complexity is dominated by the computation of exponential of large matrices. In this paper, we propose two inexact Krylov subspace algorithms for solving the large matrix exponential eigenproblem effectivel…
Université de Paris（巴黎大学）；Télécom Paris（巴黎电信学院）；IPParis（巴黎理工学院）
In this paper, we propose an implementation of both Large Deformation Diffeomorphic Metric Mapping (LDDMM) and Metamorphosis image registration using a semi-Lagrangian scheme for geodesic shooting. We propose to solve both problems as an inexact matching providing a single and unifying cost function. We demonstrate that for image registration the use of a semi-Lagrangian scheme is more stable than a standard Eulerian scheme. Our GPU implementation is based on PyTorch, which greatly simplifies and accelerates the computations thanks to its powerful automatic differentiation engine. It will be f…
We study stochastic inexact Newton methods and consider their application in nonconvex settings. Building on the work of [R. Bollapragada, R. H. Byrd, and J. Nocedal, IMA Journal of Numerical Analysis, 39 (2018), pp. 545--578] we derive bounds for convergence rates in expected value for stochastic low rank Newton methods, and stochastic inexact Newton Krylov methods. These bounds quantify the errors incurred in subsampling the Hessian and gradient, as well as in approximating the Newton linear solve, and in choosing regularization and step length parameters. We deploy these methods in training…
Moving mesh methods are designed to redistribute a mesh in a regular way. This applied problem can be considered to overlap with the problem of finding a diffeomorphic mapping between density measures. In applications, an off-the-shelf grid needs to be restructured to have higher grid density in some regions than others. This should be done in a way that avoids tangling, hence, the attractiveness of diffeomorphic mapping techniques. For exact diffeomorphic mapping on the sphere a major tool used is Optimal Transport, which allows for diffeomorphic mapping between even non-continuous source and…
This paper presents a novel numerical method for the Newton seismic full-waveform inversion (FWI). The method is based on the full-space approach, where the state, adjoint state, and control variables are optimized simultaneously. Each Newton step is formulated as a PDE-constrained optimization problem, which is cast in the form of the Karush-Kuhn-Tucker (KKT) system of linear algebraic equitations. The KKT system is solved inexactly with a preconditioned Krylov solver. We introduced two preconditioners: the one based on the block-triangular factorization and its variant with an inexact block …
Nonlinear Preconditioning: How to use a Nonlinear Schwarz Method to Precondition Newton's Method
University of Strathclyde（斯特拉斯克莱德大学）；Université de Genève（日内瓦大学）；Université Nice Sophia Antipolis（尼斯索菲亚安蒂波利斯大学）；Inria（法国国家数字科学研究所）；Hong Kong Baptist University（香港浸会大学）
In this work, we investigate various approaches that use learning from training data to solve inverse problems, following a bi-level learning approach. We consider a general framework for optimal inversion design, where training data can be used to learn optimal regularization parameters, data fidelity terms, and regularizers, thereby resulting in superior variational regularization methods. In particular, we describe methods to learn optimal $p$ and $q$ norms for ${\rm L}^p-{\rm L}^q$ regularization and methods to learn optimal parameters for regularization matrices defined by covariance kern…
