19 research outputs found
Distributed-memory large deformation diffeomorphic 3D image registration
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 solution, which poses the demand for efficient optimization methods as
well as an effective utilization of high performance computing resources. To
address this problem we use a preconditioned, inexact, Gauss-Newton- Krylov
solver. Our algorithm integrates several components: a spectral discretization
in space, a semi-Lagrangian formulation in time, analytic adjoints, different
regularization functionals (including volume-preserving ones), a spectral
preconditioner, a highly optimized distributed Fast Fourier Transform, and a
cubic interpolation scheme for the semi-Lagrangian time-stepping. We
demonstrate the scalability of our algorithm on images with resolution of up to
on the "Maverick" and "Stampede" systems at the Texas Advanced
Computing Center (TACC). The critical problem in the medical imaging
application domain is strong scaling, that is, solving registration problems of
a moderate size of ---a typical resolution for medical images. We are
able to solve the registration problem for images of this size in less than
five seconds on 64 x86 nodes of TACC's "Maverick" system.Comment: accepted for publication at SC16 in Salt Lake City, Utah, USA;
November 201
Acceleration of the PDHGM on strongly convex subspaces
We propose several variants of the primal-dual method due to Chambolle and
Pock. Without requiring full strong convexity of the objective functions, our
methods are accelerated on subspaces with strong convexity. This yields mixed
rates, with respect to initialisation and with respect to
the dual sequence, and the residual part of the primal sequence. We demonstrate
the efficacy of the proposed methods on image processing problems lacking
strong convexity, such as total generalised variation denoising and total
variation deblurring
An inexact Newton-Krylov algorithm for constrained diffeomorphic image registration
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 - or
-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.Comment: 32 pages; 10 figures; 9 table
Template-Based Image Reconstruction from Sparse Tomographic Data
Funder: University of CambridgeAbstract: We propose a variational regularisation approach for the problem of template-based image reconstruction from indirect, noisy measurements as given, for instance, in X-ray computed tomography. An image is reconstructed from such measurements by deforming a given template image. The image registration is directly incorporated into the variational regularisation approach in the form of a partial differential equation that models the registration as either mass- or intensity-preserving transport from the template to the unknown reconstruction. We provide theoretical results for the proposed variational regularisation for both cases. In particular, we prove existence of a minimiser, stability with respect to the data, and convergence for vanishing noise when either of the abovementioned equations is imposed and more general distance functions are used. Numerically, we solve the problem by extending existing Lagrangian methods and propose a multilevel approach that is applicable whenever a suitable downsampling procedure for the operator and the measured data can be provided. Finally, we demonstrate the performance of our method for template-based image reconstruction from highly undersampled and noisy Radon transform data. We compare results for mass- and intensity-preserving image registration, various regularisation functionals, and different distance functions. Our results show that very reasonable reconstructions can be obtained when only few measurements are available and demonstrate that the use of a normalised cross correlation-based distance is advantageous when the image intensities between the template and the unknown image differ substantially