ResNet-LDDMM: Advancing the LDDMM Framework Using Deep Residual Networks.

In deformable registration, the Riemannian framework - Large Deformation Diffeomorphic Metric Mapping, or LDDMM for short - has inspired numerous techniques for comparing, deforming, averaging and analyzing shapes or images. Grounded in flows of vector fields, akin to the equations of motion used in fluid dynamics, LDDMM algorithms solve the flow equation in the space of plausible deformations, i.e., diffeomorphisms. In this work, we make use of deep residual neural networks to solve the non-stationary ODE (flow equation) based on an Euler's discretization scheme. The central idea is to represent time-dependent velocity fields as fully connected ReLU neural networks (building blocks) and derive optimal weights by minimizing a regularized loss function. Computing minimizing paths between deformations, thus between shapes, turns to find optimal network parameters by back-propagating over the intermediate building blocks. Geometrically, at each time step, our algorithm searches for an optimal partition of the space into multiple polytopes, and then computes optimal velocity vectors as affine transformations on each of these polytopes. As a result, different parts of the shape, even if they are close (such as two fingers of a hand), can be made to belong to different polytopes, and therefore be moved in different directions without costing too much energy. Importantly, we show how diffeomorphic transformations, or more precisely bilipshitz transformations, are predicted by our registration algorithm. We illustrate these ideas on diverse registration problems of 3D shapes under complex topology-preserving transformations. We thus provide essential foundations for more advanced shape variability analysis under a novel joint geometric-neural networks Riemannian-like framework, i.e., ResNet-LDDMM.

Mechanistic Modeling of Longitudinal Shape Changes: Equations of Motion and Inverse Problems.

This paper examines a longitudinal shape evolution model in which a three-dimensional volume progresses through a family of elastic equilibria in response to the time-derivative of an internal force, or yank, with an additional regularization to ensure diffeomorphic transformations. We consider two different models of yank and address the long time existence and uniqueness of solutions for the equations of motion in both models. In addition, we derive sufficient conditions for the existence of an optimal yank that best describes the change from an observed initial volume to an observed volume at a later time. The main motivation for this work is the understanding of processes such as growth and atrophy in anatomical structures, where the yank could be roughly interpreted as a metabolic event triggering morphological changes. We provide preliminary results on simple examples to illustrate, under this model, the retrievability of some attributes of such events.

Computational anatomy and diffeomorphometry: A dynamical systems model of neuroanatomy in the soft condensed matter continuum.

The nonlinear systems models of computational anatomy that have emerged over the past several decades are a synthesis of three significant areas of computational science and biological modeling. First is the algebraic model of biological shape as a Riemannian orbit, a set of objects under diffeomorphic action. Second is the embedding of anatomical shapes into the soft condensed matter physics continuum via the extension of the Euler equations to geodesic, smooth flows with inverses, encoding divergence for the compressibility of atrophy and expansion of growth. Third, is making human shape and form a metrizable space via geodesic connections of coordinate systems. These three themes place our formalism into the modern data science world of personalized medicine supporting inference of high-dimensional anatomical phenotypes for studying neurodegeneration and neurodevelopment. The dynamical systems model of growth and atrophy that emerges is one which is organized in terms of forces, accelerations, velocities, and displacements, with the associated Hamiltonian momentum and the diffeomorphic flow acting as the state, and the smooth vector field the control. The forces that enter the model derive from external measurements through which the dynamical system must flow, and the internal potential energies of structures making up the soft condensed matter. We examine numerous examples on growth and atrophy. This article is categorized under: Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Imaging Models of Systems Properties and Processes > Organ, Tissue, and Physiological Models.

Diffeomorphic Surface Registration with Atrophy Constraints.

Diffeomorphic registration using optimal control on the diffeomorphism group and on shape spaces has become widely used since the development of the large deformation diffeomorphic metric mapping (LDDMM) algorithm. More recently, a series of algorithms involving sub-Riemannian constraints have been introduced in which the velocity fields that control the shapes in the LDDMM framework are constrained in accordance with a specific deformation model. Here, we extend this setting by considering, for the first time, inequality constraints in order to estimate surface deformations that only allow for atrophy, introducing for this purpose an algorithm that uses the augmented Lagrangian method. We prove the existence of solutions of the associated optimal control problem and the consistency of our approximation scheme. These developments are illustrated by numerical experiments on simulated and real data.