Groupwise Registration Algorithm Research Articles

Deep Learning Deformation Initialization for Rapid Groupwise Registration of Inhomogeneous Image Populations.

Groupwise image registration tackles biases that can potentially arise from inappropriate template selection. It typically involves simultaneous registration of a cohort of images to a common space that is not specified a priori. Existing groupwise registration methods are computationally complex and are only effective for image populations without large anatomical variations. In this paper, we propose a deep learning framework to rapidly estimate large deformations between images to significantly reduce structural variability. Specifically, we employ a multi-level graph coarsening method to agglomerate similar images into clusters, each represented by an exemplar image. We then use a deep learning framework to predict the initial deformations between images. Warping with the estimated deformations brings the images closer in the image manifold and their alignment can be further refined using conventional groupwise registration algorithms. We evaluated the effectiveness of our method in groupwise registration of MR brain images and compared it against state-of-the-art groupwise registration methods. Experimental results indicate that deformation initialization enables groupwise registration to converge significantly faster with competitive accuracy, therefore facilitates large-scale imaging studies.

A Review of Point Set Registration: From Pairwise Registration to Groupwise Registration.

This paper presents a comprehensive literature review on point set registration. The state-of-the-art modeling methods and algorithms for point set registration are discussed and summarized. Special attention is paid to methods for pairwise registration and groupwise registration. Some of the most prominent representative methods are selected to conduct qualitative and quantitative experiments. From the experiments we have conducted on 2D and 3D data, CPD-GL pairwise registration algorithm and JRMPC groupwise registration algorithm seem to outperform their rivals both in accuracy and computational complexity. Furthermore, future research directions and avenues in the area are identified.

The prospects for application of computational anatomy in forensic anthropology for sex determination

The purpose of this study is to assess the relevance of computational anatomy for the sex determination in forensic anthropology. A novel groupwise registration algorithm is used, based on keypoint extraction, able to register several hundred full body images in a common space. Experiments were conducted on 83 CT scanners of living individuals from the public VISCERAL database. In our experiments, we first verified that the well-known criteria for sex discrimination on the hip-bone were well preserved in mean images. In a second experiment, we have tested semi-automatic positioning of anatomical landmarks to measure the relevance of groupwise registration for future research. We applied the Probabilistic Sex Diagnosis tool on the predicted landmarks. This resulted in 62% of correct sex determinations, 37% of undetermined cases, and 1% of errors. The main limiting factors are the population sample size and the lack of precision for the initial manual positioning of the landmarks in the mean image. We also give insights on future works for robust and fully automatic sex determination.

A Markov random field approach to group-wise registration/mosaicing with application to ultrasound.

In this paper we present a group-wise non-rigid registration/mosaicing algorithm based on block-matching, which is developed within a probabilistic framework. The discrete form of its energy functional is linked to a Markov Random Field (MRF) containing double and triple cliques, which can be effectively optimized using modern MRF optimization algorithms popular in computer vision. Also, the registration problem is simplified by introducing a mosaicing function which partitions the composite volume into regions filled with data from unique, partially overlapping source volumes. Ultrasound confidence maps are incorporated into the registration framework in order to give accurate results in the presence of image artifacts. The algorithm is initially tested on simulated images where shadows have been generated. Also, validation results for the group-wise registration algorithm using real ultrasound data from an abdominal phantom are presented. Finally, composite obstetrics image volumes are constructed using clinical scans of pregnant subjects, where fetal movement makes registration/mosaicing especially difficult. In addition, results are presented suggesting that a fusion approach to MRF registration can produce accurate displacement fields much faster than standard approaches.

Group-Wise Registration of Point Sets for Statistical Shape Models

This paper presents a novel, fast, group-wise registration technique based on establishing soft correspondences between groups of point sets. The registration approach is used to create a statistical shape model, capable of learning the shape variations within a training set. The shape model consists of a mean shape and its transformations to all training shapes. We decouple the procedure into two steps: updating the mean shape and registering it to the training shapes. The algorithm alternates between these two steps until convergence. Following the generation of the statistical shape model, we use the soft correspondence approach to register the model to a new observation. We perform extensive experiments on two data sets: lumbar spine and hippocampi. We compare our algorithm to available state-of- the-art group-wise registration algorithms including feature-based and volume-based approaches. We demonstrate improved generalization, specificity and compactness compared to these algorithms.

Feature‐based groupwise registration by hierarchical anatomical correspondence detection

Groupwise registration has been widely investigated in recent years due to its importance in analyzing population data in many clinical applications. To our best knowledge, most of the groupwise registration algorithms only utilize the intensity information. However, it is well known that using intensity only is not sufficient to achieve the anatomically sound correspondences in medical image registration. In this article, we propose a novel feature-based groupwise registration algorithm to establish the anatomical correspondence across subjects by using the attribute vector that is defined as the morphological signature for each voxel. Similar to most of the state-of-the-art groupwise registration algorithms, which simultaneously estimate the transformation fields for all subjects, we develop an energy function to minimize the intersubject discrepancies on anatomical structures and drive all subjects toward the hidden common space. To make the algorithm efficient and robust, we decouple the complex groupwise registration problem into two easy-to-solve subproblems, namely (1) robust correspondence detection and (2) dense transformation field estimation, which are systematically integrated into a unified framework. To achieve the robust correspondences in the step (1), several strategies are adopted. First, the procedure of feature matching is evaluated within a neighborhood, rather than only on a single voxel. Second, the driving voxels with distinctive image features are designed to drive the transformations of other nondriving voxels. Third, we take advantage of soft correspondence assignment not only in the spatial domain but also across the population of subjects. Specifically, multiple correspondences are allowed to alleviate the ambiguity in establishing correspondences w.r.t. a particular subject and also the contributions from different subjects are dynamically controlled throughout the registration. Eventually in the step (2), based on the correspondences established for the driving voxels, thin-plate spline is used to propagate correspondences on the driving voxels to other locations in the image. By iteratively repeating correspondence detection and dense deformation estimation, all the subjects will be aligned onto the common space. Our feature-based groupwise registration algorithm has been extensively evaluated over 18 elderly brains, 16 brains from NIREP (with 32 manually delineated labels), 40 brains from LONI LPBA40 (with 54 manually delineated labels), and 12 pairs of normal controls and simulated atrophic brain images. In all experiments, our algorithm achieves more robust and accurate registration results, compared with another groupwise algorithm and a pairwise registration method.

Computing Accurate Correspondences across Groups of Images

Groupwise image registration algorithms seek to establish dense correspondences between sets of images. Typically, they involve iteratively improving the registration between each image and an evolving mean. A variety of methods have been proposed, which differ in their choice of objective function, representation of deformation field, and optimization methods. Given the complexity of the task, the final accuracy is significantly affected by the choices made for each component. Here, we present a groupwise registration algorithm which can take advantage of the statistics of both the image intensities and the range of shapes across the group to achieve accurate matching. By testing on large sets of images (in both 2D and 3D), we explore the effects of using different image representations and different statistical shape constraints. We demonstrate that careful choice of such representations can lead to significant improvements in overall performance.

Attribute vector guided groupwise registration

Groupwise registration has been recently introduced to simultaneously register a group of images by avoiding the selection of a particular template. To achieve this, several methods have been proposed to take advantage of information-theoretic entropy measures based on image intensity. However, simplistic utilization of voxelwise image intensity is not sufficient to establish reliable correspondences, since it lacks important contextual information. Therefore, we explore the notion of attribute vector as the voxel signature, instead of image intensity, to guide the correspondence detection in groupwise registration. In particular, for each voxel, the attribute vector is computed from its multi-scale neighborhoods, in order to capture the geometric information at different scales. The probability density function (PDF) of each element in the attribute vector is then estimated from the local neighborhood, providing a statistical summary of the underlying anatomical structure in that local pattern. Eventually, with the help of Jensen–Shannon (JS) divergence, a group of subjects can be aligned simultaneously by minimizing the sum of JS divergences across the image domain and all attributes. We have employed our groupwise registration algorithm on both real (NIREP NA0 data set) and simulated data (12 pairs of normal control and simulated atrophic data set). The experimental results demonstrate that our method yields better registration accuracy, compared with a popular groupwise registration method.

Group-wise Point-set registration using a novel CDF-based Havrda-Charvát Divergence.

This paper presents a novel and robust technique for group-wise registration of point sets with unknown correspondence. We begin by defining a Havrda-Charvát (HC) entropy valid for cumulative distribution functions (CDFs) which we dub the HC Cumulative Residual Entropy (HC-CRE). Based on this definition, we propose a new measure called the CDF-HC divergence which is used to quantify the dis-similarity between CDFs estimated from each point-set in the given population of point sets. This CDF-HC divergence generalizes the CDF based Jensen-Shannon (CDF-JS) divergence introduced earlier in the literature, but is much simpler in implementation and computationally more efficient.A closed-form formula for the analytic gradient of the cost function with respect to the non-rigid registration parameters has been derived, which is conducive for efficient quasi-Newton optimization. Our CDF-HC algorithm is especially useful for unbiased point-set atlas construction and can do so without the need to establish correspondences. Mathematical analysis and experimental results indicate that this CDF-HC registration algorithm outperforms the previous group-wise point-set registration algorithms in terms of efficiency, accuracy and robustness.

Implicit reference-based group-wise image registration and its application to structural and functional MRI

In this study, an implicit reference group-wise (IRG) registration with a small deformation, linear elastic model was used to jointly estimate correspondences between a set of MRI images. The performance of pair-wise and group-wise registration algorithms was evaluated for spatial normalization of structural and functional MRI data. Traditional spatial normalization is accomplished by group-to-reference (G2R) registration in which a group of images are registered pair-wise to a reference image. G2R registration is limited due to bias associated with selecting a reference image. In contrast, implicit reference group-wise (IRG) registration estimates correspondences between a group of images by jointly registering the images to an implicit reference corresponding to the group average. The implicit reference is estimated during IRG registration eliminating the bias associated with selecting a specific reference image. Registration performance was evaluated using segmented T1-weighted magnetic resonance images from the Nonrigid Image Registration Evaluation Project (NIREP), DTI and fMRI images. Implicit reference pair-wise (IRP) registration—a special case of IRG registration for two images—is shown to produce better relative overlap than IRG for pair-wise registration using the same small deformation, linear elastic registration model. However, IRP-G2R registration is shown to have significant transitivity error, i.e., significant inconsistencies between correspondences defined by different pair-wise transformations. In contrast, IRG registration produces consistent correspondence between images in a group at the cost of slightly reduced pair-wise RO accuracy compared to IRP-G2R. IRG spatial normalization of the fractional anisotropy (FA) maps of DTI is shown to have smaller FA variance compared with G2R methods using the same elastic registration model. Analyses of fMRI data sets with sensorimotor and visual tasks show that IRG registration, on average, increases the statistical detectability of brain activation compared to G2R registration.

Non-rigid Groupwise Registration using B-Spline Deformation Model

In this work, we extend a previously demonstrated entropy based groupwise registration method to include a non-rigid deformation model based on B-splines. We describe an open source implementation of the groupwise registration algorithm using the Insight Toolkit ITK. We provide the source code, parameters, input and output data that we used for validation.We describe an efficient implementation of the algorithm by using a stochastic optimization scheme embedded in a multi-resolution setting. The objective function is optimized using gradient descent algorithm combined with line search for the step size. The derivative of the objective function is evaluated efficiently by computing Jacobian of B-spline deformation field locally.We demonstrate the algorithm in application to different imaging modalities including proton density, FA, T1 and T2 MR images. We validate the algorithm on synthetic datasets varying from 2 to 30 images by recovering randomly applied affine and B-spline transforms.