Groupwise Registration Method Research Articles

Retrospective motion correction for cardiac multi-parametric mapping with dictionary matching-based image synthesis and a low-rank constraint.

To develop a model-based motion correction (MoCo) method that does not need an analytical signal model to improve the quality of cardiac multi-parametric mapping. The proposed method constructs a hybrid loss that includes a dictionary-matching loss and a signal low-rankness loss, where the former registers the multi-contrast original images to a set of motion-free synthetic images and the latter forces the deformed images to be spatiotemporally coherent. We compared the proposed method with non-MoCo, a pairwise registration method (Pairwise-MI), and a groupwise registration method (pTVreg) via a free-breathing Multimapping dataset of 15 healthy subjects, both quantitatively and qualitatively. The proposed method achieved the lowest contour tracking errors (epicardium: 2.00 ± 0.39 mm vs 4.93 ± 2.29 mm, 3.50 ± 1.26 mm, and 2.61 ± 1.00 mm, and endocardium: 1.84 ± 0.34 mm vs 4.93 ± 2.40 mm, 3.43 ± 1.27 mm, and 2.55 ± 1.09 mm for the proposed method, non-MoCo, Pairwise-MI, and pTVreg, respectively; all p < 0.01) and the lowest dictionary matching errors among all methods. The proposed method also achieved the highest scores on the visual quality of mapping (T1: 4.74 ± 0.33 vs 2.91 ± 0.82, 3.58 ± 0.87, and 3.97 ± 1.05, and T2: 4.48 ± 0.56 vs 2.59 ± 0.81, 3.56 ± 0.93, and 4.14 ± 0.80 for the proposed method, non-MoCo, Pairwise-MI, and pTVreg, respectively; all p < 0.01). Finally, the proposed method had similar T1 and T2 mean values and SDs relative to the breath-hold reference in nearly all myocardial segments, whereas all other methods led to significantly different T1 and T2 measures and increases of SDs in multiple segments. The proposed method significantly improves the motion correction accuracy and mapping quality compared with non-MoCo and alternative image-based methods.

Free-breathing simultaneous native myocardial T1, T2 and T1ρ mapping with Cartesian acquisition and dictionary matching

BackgroundT1, T2 and T1ρ are well-recognized parameters for quantitative cardiac MRI. Simultaneous estimation of these parameters allows for comprehensive myocardial tissue characterization, such as myocardial fibrosis and edema. However, conventional techniques either quantify the parameters individually with separate breath-hold acquisitions, which may result in unregistered parameter maps, or estimate multiple parameters in a prolonged breath-hold acquisition, which may be intolerable to patients. We propose a free-breathing multi-parametric mapping (FB-MultiMap) technique that provides co-registered myocardial T1, T2 and T1ρ maps in a single efficient acquisition. MethodsThe proposed FB-MultiMap performs electrocardiogram-triggered single-shot Cartesian acquisition over 16 consecutive cardiac cycles, where inversion, T2 and T1ρ preparations are introduced for varying contrasts. A diaphragmatic navigator was used for prospective through-plane motion correction and the in-plane motion was corrected retrospectively with a group-wise image registration method. Quantitative mapping was conducted through dictionary matching of the motion corrected images, where the subject-specific dictionary was created using Bloch simulations for a range of T1, T2 and T1ρ values, as well as B1 factors to account for B1 inhomogeneities. The FB-MultiMap was optimized and validated in numerical simulations, phantom experiments, and in vivo imaging of 15 healthy subjects and six patients with suspected cardiac diseases. ResultsThe phantom T1, T2 and T1ρ values estimated with FB-MultiMap agreed well with reference measurements with no dependency on heart rate. In healthy subjects, FB-MultiMap T1 was higher than MOLLI T1 mapping (1218 ± 50 ms vs. 1166 ± 38 ms, p < 0.001). The myocardial T2 and T1ρ estimated with FB-MultiMap were lower compared to the mapping with T2- or T1ρ-prepared 2D balanced steady-state free precession (T2: 41.2 ± 2.8 ms vs. 42.5 ± 3.1 ms, p = 0.06; T1ρ: 45.3 ± 4.4 ms vs. 50.2 ± 4.0, p < 0.001). The pathological changes in myocardial parameters measured with FB-MultiMap were consistent with conventional techniques in all patients. ConclusionThe proposed free-breathing multi-parametric mapping technique provides co-registered myocardial T1, T2 and T1ρ maps in 16 heartbeats, achieving similar mapping quality to conventional breath-hold mapping methods.

Image registration: Maximum likelihood, minimum entropy and deep learning.

In this work, we propose a theoretical framework based on maximum profile likelihood for pairwise and groupwise registration. By an asymptotic analysis, we demonstrate that maximum profile likelihood registration minimizes an upper bound on the joint entropy of the distribution that generates the joint image data. Further, we derive the congealing method for groupwise registration by optimizing the profile likelihood in closed form, and using coordinate ascent, or iterative model refinement. We also describe a method for feature based registration in the same framework and demonstrate it on groupwise tractographic registration. In the second part of the article, we propose an approach to deep metric registration that implements maximum likelihood registration using deep discriminative classifiers. We show further that this approach can be used for maximum profile likelihood registration to discharge the need for well-registered training data, using iterative model refinement. We demonstrate that the method succeeds on a challenging registration problem where the standard mutual information approach does not perform well.

Groupwise registration with global-local graph shrinkage in atlas construction.

Graph-based groupwise registration methods are widely used in atlas construction. Given a group of images, a graph is built whose nodes represent the images, and whose edges represent a geodesic path between two nodes. The distribution of images on an image manifold is explored through edge traversal in a graph. The final atlas is a mean image at the population center of the distribution on the manifold. The procedure of warping all images to the mean image turns to dynamic graph shrinkage in which nodes become closer to each other. Most conventional groupwise registration frameworks construct and shrink a graph without considering the local distribution of images on the dataset manifold and the local structure variations between image pairs. Neglecting the local information fundamentally decrease the accuracy and efficiency when population atlases are built for organs with large inter-subject anatomical variabilities. To overcome the problem, this paper proposes a global-local graph shrinkage approach that can generate accurate atlas. A connected graph is constructed automatically based on global similarities across the images to explore the global distribution. A local image distribution obtained by image clustering is used to simplify the edges of the constructed graph. Subsequently, local image similarities refine the deformation estimated through global image similarity for each image warping along the graph edges. Through the image warping, the overall simplified graph shrinks gradually to yield the atlas with respecting both global and local features. The proposed method is evaluated on 61 synthetic and 20 clinical liver datasets, and the results are compared with those of six state-of-the-art groupwise registration methods. The experimental results show that the proposed method outperforms non-global-local method approaches in terms of accuracy.

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.

Feature-based groupwise registration of historical aerial images to present-day ortho-photo maps

In this paper, we address the registration of historical WWII images to present-day ortho-photo maps for the purpose of geolocalization. Due to the challenging nature of this problem, we propose to register the images jointly as a group rather than in a step-by-step manner. To this end, we exploit Hough voting spaces as pairwise registration estimators and show how they can be integrated into a probabilistic groupwise registration framework that can be efficiently optimized. The feature-based nature of our registration framework allows to register images with a-priori unknown translational and rotational relations, and is also able to handle scale changes of up to 30% in our test data due to a final geometrically guided matching step. The superiority of the proposed method over existing pairwise and groupwise registration methods is demonstrated on eight highly challenging sets of historical images with corresponding ortho-photo maps.

A Groupwise Registration Method Based on Topology Center of Images

A Groupwise Registration Method Based on Topology Center of Images

Efficient Groupwise Registration of MR Brain Images via Hierarchical Graph Set Shrinkage.

Accurate and efficient groupwise registration is important for population analysis. Current groupwise registration methods suffer from high computational cost, which hinders their application to large image datasets. To alleviate the computational burden while delivering accurate groupwise registration result, we propose to use a hierarchical graph set to model the complex image distribution with possibly large anatomical variations, and then turn the groupwise registration problem as a series of simple-to-solve graph shrinkage problems. Specifically, first, we divide the input images into a set of image clusters hierarchically, where images within each image cluster have similar anatomical appearances whereas images falling into different image clusters have varying anatomical appearances. After clustering, two types of graphs, i.e., intra-graph and inter-graph, are employed to hierarchically model the image distribution both within and across the image clusters. The constructed hierarchical graph set divides the registration problem of the whole image set into a series of simple-to-solve registration problems, where the entire registration process can be solved accurately and efficiently. The final deformation pathway of each image to the estimated population center can be obtained by composing each part of the deformation pathway along the hierarchical graph set. To evaluate our proposed method, we performed registration of a hundred of brain images with large anatomical variations. The results indicate that our method yields significant improvement in registration performance over state-of-the-art groupwise registration methods.

Description of an isoniazid-resistant tuberculosis outbreak in a block of apartments

It is fundamentally important to fuse the brain atlas from magnetic resonance (MR) images for many imaging-based studies. Most existing works focus on fusing the atlases from high-quality MR images. However, for low-quality diagnostic images (i.e., with high inter-slice thickness), the problem of atlas fusion has not been addressed yet. In this paper, we intend to fuse the brain atlas from the high-thickness diagnostic MR images that are prevalent for clinical routines. The main idea of our works is to extend the conventional groupwise registration by incorporating a novel super-resolution strategy. The contribution of the proposed super-resolution framework is two-fold. First, each high-thickness subject image is reconstructed to be isotropic by the patch-based sparsity learning. Then, the reconstructed isotropic image is enhanced for better quality through the random-forest-based regression model. In this way, the images obtained by the super-resolution strategy can be fused together by applying the groupwise registration method to construct the required atlas. Our experiments have shown that the proposed framework can effectively solve the problem of atlas fusion from the low-quality brain MR images.

Robust motion correction for myocardial T1 and extracellular volume mapping by principle component analysis-based groupwise image registration.

Myocardial tissue characterization by MR T1 and extracellular volume (ECV) mapping has demonstrated clinical value. The modified Look-Locker inversion recovery (MOLLI) sequence is a standard mapping technique, but its quality can be negatively affected by motion. To develop a robust motion correction method for T1 and ECV mapping. Retrospective analysis of clinical data. Fifty patients who were referred to cardiac MR exam for T1 mapping. 3.0T cardiac MRI with precontrast and postcontrast MOLLI acquisition of the left ventricle (LV). A groupwise registration method based on principle component analysis (PCA) was developed to register all MOLLI frames simultaneously. The resulting T1 and ECV maps were compared to those from the original and motion-corrected MOLLI with pairwise registration, in terms of standard deviation (SD) error. Paired variables were compared using the Wilcoxon signed-rank test. The groupwise registration method demonstrated improved registration performance compared to pairwise registration, with the T1 SD error reduced from 31 ± 20 msec to 26 ± 15 msec (P < 0.05), and ECV SD error reduced from 4.1 ± 3.6% to 2.8 ± 2.0% (P < 0.05). In LV segmental analysis, the performance was particularly improved in lateral segments, which are most affected by motion. The running time of groupwise registration was significantly shorter than that of the pairwise registration, 17.5 ± 3.0 seconds compared to 43.5 ± 2.2 seconds (P < 0.05). We developed an automatic, robust motion correction method for myocardial T1 and ECV mapping based on a new groupwise registration scheme. The method led to lower mapping error compared to the conventional pairwise registration method in reduced execution time. 3 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2018;47:1397-1405.

Evaluation of motion correction for clinical dynamic contrast enhanced MRI of the liver

Motion correction of 4D dynamic contrast enhanced MRI (DCE-MRI) series is required for diagnostic evaluation of liver lesions. The registration, however, is a challenging task, owing to rapid changes in image appearance. In this study, two different registration approaches are compared; a conventional pairwise method applying mutual information as metric and a groupwise method applying a principal component analysis based metric, introduced by Huizinga et al (2016). The pairwise method transforms the individual 3D images one by one to a reference image, whereas the groupwise registration method computes the metric on all the images simultaneously, exploiting the temporal information, and transforms all 3D images to a common space. The performance of the two registration methods was evaluated using 70 clinical 4D DCE-MRI series with the focus on the liver. The evaluation was based on the smoothness of the time intensity curves in lesions, lesion volume change after deformation and the smoothness of spatial deformation. Furthermore, the visual quality of subtraction images (pre-contrast image subtracted from the post contrast images) before and after registration was rated by two observers. Both registration methods improved the alignment of the DCE-MRI images in comparison to the non-corrected series. Furthermore, the groupwise method achieved better temporal alignment with smoother spatial deformations than the pairwise method. The quality of the subtraction images was graded satisfactory in 32% of the cases without registration and in 77% and 80% of the cases after pairwise and groupwise registration, respectively. In conclusion, the groupwise registration method outperforms the pairwise registration method and achieves clinically satisfying results. Registration leads to improved subtraction images.

Efficient Groupwise Registration for Brain MRI by Fast Initialization.

Groupwise image registration provides an unbiased registration solution upon a population of images, which can facilitate the subsequent population analysis. However, it is generally computationally expensive for performing groupwise registration on a large set of images. To alleviate this issue, we propose to utilize a fast initialization technique for speeding up the groupwise registration. Our main idea is to generate a set of simulated brain MRI samples with known deformations to their group center. This can be achieved in the training stage by two steps. First, a set of training brain MR images is registered to their group center with a certain existing groupwise registration method. Then, in order to augment the samples, we perform PCA on the set of obtained deformation fields (to the group center) to parameterize the deformation fields. In doing so, we can generate a large number of deformation fields, as well as their respective simulated samples using different parameters for PCA. In the application stage, when given a new set of testing brain MR images, we can mix them with the augmented training samples. Then, for each testing image, we can find its closest sample in the augmented training dataset for fast estimating its deformation field to the group center of the training set. In this way, a tentative group center of the testing image set can be immediately estimated, and the deformation field of each testing image to this estimated group center can be obtained. With this fast initialization for groupwise registration of testing images, we can finally use an existing groupwise registration method to quickly refine the groupwise registration results. Experimental results on ADNI dataset show the significantly improved computational efficiency and competitive registration accuracy, compared to state-of-the-art groupwise registration methods.

Brain atlas fusion from high-thickness diagnostic magnetic resonance images by learning-based super-resolution

It is fundamentally important to fuse the brain atlas from magnetic resonance (MR) images for many imaging-based studies. Most existing works focus on fusing the atlases from high-quality MR images. However, for low-quality diagnostic images (i.e., with high inter-slice thickness), the problem of atlas fusion has not been addressed yet. In this paper, we intend to fuse the brain atlas from the high-thickness diagnostic MR images that are prevalent for clinical routines. The main idea of our works is to extend the conventional groupwise registration by incorporating a novel super-resolution strategy. The contribution of the proposed super-resolution framework is two-fold. First, each high-thickness subject image is reconstructed to be isotropic by the patch-based sparsity learning. Then, the reconstructed isotropic image is enhanced for better quality through the random-forest-based regression model. In this way, the images obtained by the super-resolution strategy can be fused together by applying the groupwise registration method to construct the required atlas. Our experiments have shown that the proposed framework can effectively solve the problem of atlas fusion from the low-quality brain MR images.

EHUGS: Enhanced Hierarchical Unbiased Graph Shrinkage for Efficient Groupwise Registration.

Effective and efficient spatial normalization of a large population of brain images is critical for many clinical and research studies, but it is technically very challenging. A commonly used approach is to choose a certain image as the template and then align all other images in the population to this template by applying pairwise registration. To avoid the potential bias induced by the inappropriate template selection, groupwise registration methods have been proposed to simultaneously register all images to a latent common space. However, current groupwise registration methods do not make full use of image distribution information for more accurate registration. In this paper, we present a novel groupwise registration method that harnesses the image distribution information by capturing the image distribution manifold using a hierarchical graph with its nodes representing the individual images. More specifically, a low-level graph describes the image distribution in each subgroup, and a high-level graph encodes the relationship between representative images of subgroups. Given the graph representation, we can register all images to the common space by dynamically shrinking the graph on the image manifold. The topology of the entire image distribution is always maintained during graph shrinkage. Evaluations on two datasets, one for 80 elderly individuals and one for 285 infants, indicate that our method can yield promising results.

Dual-Layer Groupwise Registration for Consistent Labeling of Longitudinal Brain Images.

The growing collection of longitudinal images for brain disease diagnosis necessitates the development of advanced longitudinal registration and anatomical labeling methods that can respect temporal consistency between images. However, the characteristics of such longitudinal images and how they lodge into the image manifold are often neglected in existing labeling methods. Indeed, most of them independently align atlases to each target time-point image for propagating the pre-defined atlas labels to the subject domain. In this paper, we present a dual-layer groupwise registration method to consistently label anatomical regions of interest in brain images across different time-points using a multi-atlases-based labeling framework. Our framework can best enhance the labeling of longitudinal images through: (1) using the group mean of the longitudinal images of each subject (i.e., subject-mean) as a bridge between atlases and the longitudinal subject scans to align atlases to all time-point images jointly; and (2) using inter-atlas relationship in their nesting manifold to better register each atlas image to the subject-mean. These steps yield to a more consistent (from the joint alignment of atlases with all time-point images) and more accurate (from the manifold-guided registration between each atlases and the subject-mean image) registration, thereby eventually improving the consistency and accuracy for the subsequent labeling step. We have tested our dual-layer groupwise registration method to label two challenging longitudinal brain datasets (i.e., healthy infants and Alzheimer's disease subjects). Our experimental results have showed that our method achieves higher labeling accuracy while keeping the labeling consistency over time, when compared to the traditional registration scheme (without our proposed contributions). Moreover, the proposed framework can flexibly integrate with the existing label fusion methods, such as sparse-patch based methods, to improve the labeling accuracy of longitudinal datasets.

PCA-based groupwise image registration for quantitative MRI.

Quantitative magnetic resonance imaging (qMRI) is a technique for estimating quantitative tissue properties, such as the T1 and T2 relaxation times, apparent diffusion coefficient (ADC), and various perfusion measures. This estimation is achieved by acquiring multiple images with different acquisition parameters (or at multiple time points after injection of a contrast agent) and by fitting a qMRI signal model to the image intensities. Image registration is often necessary to compensate for misalignments due to subject motion and/or geometric distortions caused by the acquisition. However, large differences in image appearance make accurate image registration challenging. In this work, we propose a groupwise image registration method for compensating misalignment in qMRI. The groupwise formulation of the method eliminates the requirement of choosing a reference image, thus avoiding a registration bias. The method minimizes a cost function that is based on principal component analysis (PCA), exploiting the fact that intensity changes in qMRI can be described by a low-dimensional signal model, but not requiring knowledge on the specific acquisition model. The method was evaluated on 4D CT data of the lungs, and both real and synthetic images of five different qMRI applications: T1 mapping in a porcine heart, combined T1 and T2 mapping in carotid arteries, ADC mapping in the abdomen, diffusion tensor mapping in the brain, and dynamic contrast-enhanced mapping in the abdomen. Each application is based on a different acquisition model. The method is compared to a mutual information-based pairwise registration method and four other state-of-the-art groupwise registration methods. Registration accuracy is evaluated in terms of the precision of the estimated qMRI parameters, overlap of segmented structures, distance between corresponding landmarks, and smoothness of the deformation. In all qMRI applications the proposed method performed better than or equally well as competing methods, while avoiding the need to choose a reference image. It is also shown that the results of the conventional pairwise approach do depend on the choice of this reference image. We therefore conclude that our groupwise registration method with a similarity measure based on PCA is the preferred technique for compensating misalignments in qMRI.

Low-Rank Atlas Image Analyses in the Presence of Pathologies.

We present a common framework, for registering images to an atlas and for forming an unbiased atlas, that tolerates the presence of pathologies such as tumors and traumatic brain injury lesions. This common framework is particularly useful when a sufficient number of protocol-matched scans from healthy subjects cannot be easily acquired for atlas formation and when the pathologies in a patient cause large appearance changes. Our framework combines a low-rank-plus-sparse image decomposition technique with an iterative, diffeomorphic, group-wise image registration method. At each iteration of image registration, the decomposition technique estimates a "healthy" version of each image as its low-rank component and estimates the pathologies in each image as its sparse component. The healthy version of each image is used for the next iteration of image registration. The low-rank and sparse estimates are refined as the image registrations iteratively improve. For unbiased atlas formation, at each iteration, the average of the low-rank images from the patients is used as the atlas image for the next iteration, until convergence. Since each iteration's atlas is comprised of low-rank components, it provides a population-consistent, pathology-free appearance. Evaluations of the proposed methodology are presented using synthetic data as well as simulated and clinical tumor MRI images from the brain tumor segmentation (BRATS) challenge from MICCAI 2012.

Robust estimation of group-wise cortical correspondence with an application to macaque and human neuroimaging studies.

We present a novel group-wise registration method for cortical correspondence for local cortical thickness analysis in human and non-human primate neuroimaging studies. The proposed method is based on our earlier template based registration that estimates a continuous, smooth deformation field via sulcal curve-constrained registration employing spherical harmonic decomposition of the deformation field. This pairwise registration though results in a well-known template selection bias, which we aim to overcome here via a group-wise approach. We propose the use of an unbiased ensemble entropy minimization following the use of the pairwise registration as an initialization. An individual deformation field is then iteratively updated onto the unbiased average. For the optimization, we use metrics specific for cortical correspondence though all of these are straightforwardly extendable to the generic setting: The first focused on optimizing the correspondence of automatically extracted sulcal landmarks and the second on that of sulcal depth property maps. We further propose a robust entropy metric and a hierarchical optimization by employing spherical harmonic basis orthogonality. We also provide the detailed methodological description of both our earlier work and the proposed method with a set of experiments on a population of human and non-human primate subjects. In the experiment, we have shown that our method achieves superior results on consistency through quantitative and visual comparisons as compared to the existing methods.

Multi-atlas segmentation with particle-based group-wise image registration.

We propose a novel multi-atlas segmentation method that employs a group-wise image registration method for the brain segmentation on rodent magnetic resonance (MR) images. The core element of the proposed segmentation is the use of a particle-guided image registration method that extends the concept of particle correspondence into the volumetric image domain. The registration method performs a group-wise image registration that simultaneously registers a set of images toward the space defined by the average of particles. The particle-guided image registration method is robust with low signal-to-noise ratio images as well as differing sizes and shapes observed in the developing rodent brain. Also, the use of an implicit common reference frame can prevent potential bias induced by the use of a single template in the segmentation process. We show that the use of a particle guided-image registration method can be naturally extended to a novel multi-atlas segmentation method and improves the registration method to explicitly use the provided template labels as an additional constraint. In the experiment, we show that our segmentation algorithm provides more accuracy with multi-atlas label fusion and stability against pair-wise image registration. The comparison with previous group-wise registration method is provided as well.

Intensity and sulci landmark combined brain atlas construction for Chinese pediatric population

Constructing an atlas from a population of brain images is of vital importance to medical image analysis. Especially in neuroscience study, creating a brain atlas is useful for intra- and inter-population comparison. Research on brain atlas construction has attracted great attention in recent years, but the research on pediatric population is still limited, mainly due to the limited availability and the relatively low quality of pediatric magnetic resonance brain images. This article is targeted at creating a high quality representative brain atlas for Chinese pediatric population. To achieve this goal, we have designed a set of preprocessing procedures to improve the image quality and developed an intensity and sulci landmark combined groupwise registration method to align the population of images for atlas construction. As demonstrated in experiments, the newly constructed atlas can better represent the size and shape of brains of Chinese pediatric population, and show better performance in Chinese pediatric brain image analysis compared with other standard atlases.