44,520 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
Diffeomorphic density registration
In this book chapter we study the Riemannian Geometry of the density
registration problem: Given two densities (not necessarily probability
densities) defined on a smooth finite dimensional manifold find a
diffeomorphism which transforms one to the other. This problem is motivated by
the medical imaging application of tracking organ motion due to respiration in
Thoracic CT imaging where the fundamental physical property of conservation of
mass naturally leads to modeling CT attenuation as a density. We will study the
intimate link between the Riemannian metrics on the space of diffeomorphisms
and those on the space of densities. We finally develop novel computationally
efficient algorithms and demonstrate there applicability for registering RCCT
thoracic imaging.Comment: 23 pages, 6 Figures, Chapter for a Book on Medical Image Analysi
Weighted Diffeomorphic Density Matching with Applications to Thoracic Image Registration
In this article we study the problem of thoracic image registration, in
particular the estimation of complex anatomical deformations associated with
the breathing cycle. Using the intimate link between the Riemannian geometry of
the space of diffeomorphisms and the space of densities, we develop an image
registration framework that incorporates both the fundamental law of
conservation of mass as well as spatially varying tissue compressibility
properties. By exploiting the geometrical structure, the resulting algorithm is
computationally efficient, yet widely general.Comment: Accepted in Proceedings of the 5th MICCAI workshop on Mathematical
Foundations of Computational Anatomy, Munich, Germany, 2015
(http://www-sop.inria.fr/asclepios/events/MFCA15/
Intersubject Regularity in the Intrinsic Shape of Human V1
Previous studies have reported considerable intersubject variability in the three-dimensional geometry of the human primary visual cortex (V1). Here we demonstrate that much of this variability is due to extrinsic geometric features of the cortical folds, and that the intrinsic shape of V1 is similar across individuals. V1 was imaged in ten ex vivo human hemispheres using high-resolution (200 Îźm) structural magnetic resonance imaging at high field strength (7 T). Manual tracings of the stria of Gennari were used to construct a surface representation, which was computationally flattened into the plane with minimal metric distortion. The instrinsic shape of V1 was determined from the boundary of the planar representation of the stria. An ellipse provided a simple parametric shape model that was a good approximation to the boundary of flattened V1. The aspect ration of the best-fitting ellipse was found to be consistent across subject, with a mean of 1.85 and standard deviation of 0.12. Optimal rigid alignment of size-normalized V1 produced greater overlap than that achieved by previous studies using different registration methods. A shape analysis of published macaque data indicated that the intrinsic shape of macaque V1 is also stereotyped, and similar to the human V1 shape. Previoud measurements of the functional boundary of V1 in human and macaque are in close agreement with these results
Finite element surface registration incorporating curvature, volume preservation, and statistical model information
We present a novel method for nonrigid registration of 3D surfaces and images. The method can be used to register surfaces by means of their distance images, or to register medical images directly. It is formulated as a minimization problem of a sum of several terms representing the desired properties of a registration result: smoothness, volume preservation, matching of the surface, its curvature, and possible other feature images, as well as consistency with previous registration results of similar objects, represented by a statistical deformation model. While most of these concepts are already known, we present a coherent continuous formulation of these constraints, including the statistical deformation model. This continuous formulation renders the registration method independent of its discretization. The finite element discretization we present is, while independent of the registration functional, the second main contribution of this paper. The local discontinuous Galerkin method has not previously been used in image registration, and it provides an efficient and general framework to discretize each of the terms of our functional. Computational efficiency and modest memory consumption are achieved thanks to parallelization and locally adaptive mesh refinement. This allows for the first time the use of otherwise prohibitively large 3D statistical deformation models
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