Diffeomorphic Iterative Centroid Methods for Template Estimation on Large Datasets

International audienceA common approach for analysis of anatomical variability relies on the stimation of a template representative of the population. The Large Deformation Diffeomorphic Metric Mapping is an attractive framework for that purpose. However, template estimation using LDDMM is computationally expensive, which is a limitation for the study of large datasets. This paper presents an iterative method which quickly provides a centroid of the population in the shape space. This centroid can be used as a rough template estimate or as initialization of a template estimation method. The approach is evaluated on datasets of real and synthetic hippocampi segmented from brain MRI. The results show that the centroid is correctly centered within the population and is stable for different orderings of subjects. When used as an initialization, the approach allows to substantially reduce the computation time of template estimation

Craniofacial reconstruction as a prediction problem using a Latent Root Regression model

International audienceIn this paper, we present a computer-assisted method for facial reconstruction. This method provides an estimation of the facial shape associated with unidentified skeletal remains. Current computer-assisted methods using a statistical framework rely on a common set of extracted points located on the bone and soft-tissue surfaces. Most of the facial reconstruction methods then consist of predicting the position of the soft-tissue surface points, when the positions of the bone surface points are known. We propose to use Latent Root Regression for prediction. The results obtained are then compared to those given by Principal Components Analysis linear models. In conjunction, we have evaluated the influence of the number of skull landmarks used. Anatomical skull landmarks are completed iteratively by points located upon geodesics which link these anatomical landmarks, thus enabling us to artificially increase the number of skull points. Facial points are obtained using a mesh-matching algorithm between a common reference mesh and individual soft-tissue surface meshes. The proposed method is validated in term of accuracy, based on a leave-one-out cross-validation test applied to a homogeneous database. Accuracy measures are obtained by computing the distance between the original face surface and its reconstruction. Finally, these results are discussed referring to current computer-assisted reconstruction facial techniques

Fast Template-based Shape Analysis using Diffeomorphic Iterative Centroid

International audienceA common approach for the analysis of anatomical variability relies on the estimation of a representative template of the population, followed by the study of this population based on the parameters of the deformations going from the template to the population. The Large Deformation Diffeomorphic Metric Mapping framework is widely used for shape analysis of anatomical structures, but computing a template with such framework is computationally expensive. In this paper we propose a fast approach for template-based analysis of anatomical variability. The template is estimated using a recently proposed iterative approach which quickly provides a centroid of the population. Statistical analysis is then performed using Kernel-PCA on the initial momenta that define the deformations between the centroid and each subject of the population. This approach is applied to the analysis of hippocampal shape on 80 patients with Alzheimer's Disease and 138 controls from the ADNI database

Landmark Matching via Large Deformation Diffeomorphisms on the Sphere

International audienceThis paper presents a methodology and algorithm for generating diffeomorphisms of the sphere onto itself, given the displacements of a finite set of template landmarks. Deformation maps are constructed by integration of velocity fields that minimize a quadratic smoothness energy under the specified landmark constraints. We present additional formulations of this problem which incorporate a given error variance in the positions of the landmarks. Finally, some experimental results are presented. This work has application in brain mapping, where surface data is typically mapped to the sphere as a common coordinate system

Matrix-valued Kernels for Shape Deformation Analysis

The main purpose of this paper is providing a systematic study and classification of non-scalar kernels for Reproducing Kernel Hilbert Spaces (RKHS), to be used in the analysis of deformation in shape spaces endowed with metrics induced by the action of groups of diffeomorphisms. After providing an introduction to matrix-valued kernels and their relevant differential properties, we explore extensively those, that we call TRI kernels, that induce a metric on the corresponding Hilbert spaces of vector fields that is both translation- and rotation-invariant. These are analyzed in an effective manner in the Fourier domain, where the characterization of RKHS of curl-free and divergence-free vector fields is particularly natural. A simple technique for constructing generic matrix-valued kernels from scalar kernels is also developed. We accompany the exposition of the theory with several examples, and provide numerical results that show the dynamics induced by different choices of TRI kernels on the manifold of labeled landmark points

A local technique based on vectorized surfaces for craniofacial reconstruction

International audienceIn this paper, we focus on the automation of facial reconstruction. Since they consider the whole head as the object of interest, usual reconstruction techniques are global and involve a large number of parameters to be estimated. We present a local technique which aims at reaching a good trade-off between bias and variance following the paradigm of non-parametric statistics. The estimation is localized on patches delimited by surface geodesics between anatomical points of the skull. The technique relies on a continuous representation of the individual surfaces embedded in the vectorial space of extended normal vector fields. This allows to compute deformations and averages of surfaces. It consists in estimating the soft-tissue surface over patches. Using a homogeneous database described in [31], we obtain results on the chin and nasal regions with an average error below 1 mm, outperforming the global reconstruction techniques

Giga-scale Kernel Matrix Vector Multiplication on GPU

Kernel matrix-vector multiplication (KMVM) is a foundational operation in machine learning and scientific computing. However, as KMVM tends to scale quadratically in both memory and time, applications are often limited by these computational constraints. In this paper, we propose a novel approximation procedure coined \textit{Faster-Fast and Free Memory Method} ($\text{F}^3$M) to address these scaling issues of KMVM for tall~($10^8\sim 10^9$) and skinny~($D\leq7$) data. Extensive experiments demonstrate that $\text{F}^3$M has empirical \emph{linear time and memory} complexity with a relative error of order $10^{-3}$ and can compute a full KMVM for a billion points \emph{in under a minute} on a high-end GPU, leading to a significant speed-up in comparison to existing CPU methods. We demonstrate the utility of our procedure by applying it as a drop-in for the state-of-the-art GPU-based linear solver FALKON, \emph{improving speed 1.5-5.5 times} at the cost of $<1\%$ drop in accuracy. We further demonstrate competitive results on \emph{Gaussian Process regression} coupled with significant speedups on a variety of real-world datasets

Diffeomorphic metric surface mapping in subregion of the superior temporal gyrus.

International audienceThis paper describes the application of large deformation diffeomorphic metric mapping to cortical surfaces based on the shape and geometric properties of subregions of the superior temporal gyrus in the human brain. The anatomical surfaces of the cortex are represented as triangulated meshes. The diffeomorphic matching algorithm is implemented by defining a norm between the triangulated meshes, based on the algorithms of Vaillant and Glaunès. The diffeomorphic correspondence is defined as a flow of the extrinsic three dimensional coordinates containing the cortical surface that registers the initial and target geometry by minimizing the norm. The methods are demonstrated in 40 high-resolution MRI cortical surfaces of planum temporale (PT) constructed from subsets of the superior temporal gyrus (STG). The effectiveness of the algorithm is demonstrated via the Euclidean positional distance, distance of normal vectors, and curvature before and after the surface matching as well as the comparison with a landmark matching algorithm. The results demonstrate that both the positional and shape variability of the anatomical configurations are being represented by the diffeomorphic maps

Statistical models for deformable templates in image and shape analysis (Modèles statistiques d'atlas déformables pour l'analyse d'images et de formes)

International audienceLes données de grande dimensions sont de plus en plus fréquemment collectées dans de nombreux domaines d'application. Il devient alors particulièrement important d'être capable d'extraire des caractéristiques significatives de ces bases de données. Le modèle d'atlas déformable (Deformable template model) est un outil maintenant répandu pour atteindre ce but. Cet article présente un panorama des aspects statistiques de ce modèle ainsi que ses généralisations. Nous décrivons les différents cadres mathématiques permettant de prendre en compte des types variés de données et de déformations. Nous rappelons les propriétés théoriques de convergence des estimateurs et des algorithmes permettant l'estimation de ces caractéristiques. Nous terminons cet article par la présentation de quelques résultats publiés utilisant des données réelles