Soliton Dynamics in Computational Anatomy

Computational anatomy (CA) has introduced the idea of anatomical structures being transformed by geodesic deformations on groups of diffeomorphisms. Among these geometric structures, landmarks and image outlines in CA are shown to be singular solutions of a partial differential equation that is called the geodesic EPDiff equation. A recently discovered momentum map for singular solutions of EPDiff yields their canonical Hamiltonian formulation, which in turn provides a complete parameterization of the landmarks by their canonical positions and momenta. The momentum map provides an isomorphism between landmarks (and outlines) for images and singular soliton solutions of the EPDiff equation. This isomorphism suggests a new dynamical paradigm for CA, as well as new data representation.Comment: published in NeuroImag

Imaging Informatics and the Human Brain Project: the Role of Structure, Review

(no abstract

Symmetric image registration with directly calculated inverse deformation field

This paper presents a novel technique for a symmetric deformable image registration based on a new method for fast and accurate direct inversion of a large motion model deformation field. The proposed image registration algorithm maintain a one-to-one mapping between registered images by symmetrically warping them to each other, and by ensuring the inverse consistency criterion at each iteration. This makes the final estimation of forward and backward deformation fields anatomically plausible. The quantitative validation of the method has been performed on magnetic resonance data obtained for a pelvis area demonstrating applicability of the method to adaptive prostate radiotherapy. The experiments demonstrate the improved robustness in terms of inverse consistency error when compared to previously proposed methods for symmetric image registration

Towards multiple 3D bone surface identification and reconstruction using few 2D X-ray images for intraoperative applications

This article discusses a possible method to use a small number, e.g. 5, of conventional 2D X-ray images to reconstruct multiple 3D bone surfaces intraoperatively. Each bone’s edge contours in X-ray images are automatically identified. Sparse 3D landmark points of each bone are automatically reconstructed by pairing the 2D X-ray images. The reconstructed landmark point distribution on a surface is approximately optimal covering main characteristics of the surface. A statistical shape model, dense point distribution model (DPDM), is then used to fit the reconstructed optimal landmarks vertices to reconstruct a full surface of each bone separately. The reconstructed surfaces can then be visualised and manipulated by surgeons or used by surgical robotic systems

Phenomenological model of diffuse global and regional atrophy using finite-element methods

The main goal of this work is the generation of ground-truth data for the validation of atrophy measurement techniques, commonly used in the study of neurodegenerative diseases such as dementia. Several techniques have been used to measure atrophy in cross-sectional and longitudinal studies, but it is extremely difficult to compare their performance since they have been applied to different patient populations. Furthermore, assessment of performance based on phantom measurements or simple scaled images overestimates these techniques' ability to capture the complexity of neurodegeneration of the human brain. We propose a method for atrophy simulation in structural magnetic resonance (MR) images based on finite-element methods. The method produces cohorts of brain images with known change that is physically and clinically plausible, providing data for objective evaluation of atrophy measurement techniques. Atrophy is simulated in different tissue compartments or in different neuroanatomical structures with a phenomenological model. This model of diffuse global and regional atrophy is based on volumetric measurements such as the brain or the hippocampus, from patients with known disease and guided by clinical knowledge of the relative pathological involvement of regions and tissues. The consequent biomechanical readjustment of structures is modelled using conventional physics-based techniques based on biomechanical tissue properties and simulating plausible tissue deformations with finite-element methods. A thermoelastic model of tissue deformation is employed, controlling the rate of progression of atrophy by means of a set of thermal coefficients, each one corresponding to a different type of tissue. Tissue characterization is performed by means of the meshing of a labelled brain atlas, creating a reference volumetric mesh that will be introduced to a finite-element solver to create the simulated deformations. Preliminary work on the simulation of acquisition artefa- - cts is also presented. Cross-sectional and

Model-Based Identification of Anatomical Boundary Conditions in Living Tissues

International audienceIn this paper, we present a novel method dealing with the identification of boundary conditions of a deformable organ, a particularly important step for the creation of patient-specific biomechani-cal models of the anatomy. As an input, the method requires a set of scans acquired in different body positions. Using constraint-based finite element simulation, the method registers the two data sets by solving an optimization problem minimizing the energy of the deformable body while satisfying the constraints located on the surface of the registered organ. Once the equilibrium of the simulation is attained (i.e. the organ registration is computed), the surface forces needed to satisfy the constraints provide a reliable estimation of location, direction and magnitude of boundary conditions applied to the object in the deformed position. The method is evaluated on two abdominal CT scans of a pig acquired in flank and supine positions. We demonstrate that while computing a physically admissible registration of the liver, the resulting constraint forces applied to the surface of the liver strongly correlate with the location of the anatomical boundary conditions (such as contacts with bones and other organs) that are visually identified in the CT images

Toward adaptive radiotherapy for head and neck patients: Uncertainties in dose warping due to the choice of deformable registration algorithm.

The aims of this work were to evaluate the performance of several deformable image registration (DIR) algorithms implemented in our in-house software (NiftyReg) and the uncertainties inherent to using different algorithms for dose warping

Statistically-Constrained High-Dimensional Warping Using Wavelet-Based Priors

In this paper, a Statistical Model of Deformation (SMD) that captures the statistical prior distribution of high-dimensional deformations more accurately and effectively than conventional PCA-based statistical shape models is used to regularize deformable registration. SMD utilizes a wavelet-based representation of statistical variation of a deformation field and its Jacobian, and it is able to capture both global and fine shape detail without overconstraining the deformation process. This approach is shown to produce more accurate and robust registration results in MR brain images, relative to the registration methods that use Laplacian-based smoothness constraints of deformation fields. In experiments, we evaluate the SMD-constrained registration by comparing the performance of registration with and without SMD in a specific deformable registration framework. The proposed method can potentially incorporate various registration algorithms to improve their robustness and stability using statistically-based regularization