We present an information-theoretic approach to registration of DWI with explicit optimization over the orientational scale, with an additional focus on normalized mutual information as a robust information-theoretic similarity measure for DWI. The framework is an extension of the LOR-DWI density-based hierarchical scale-space model, that varies and optimizes over the integration, spatial, directional, and intensity scales. We extend the model to non-rigid deformations and show that the formulation provides intrinsic regularization through the orientational information. Our experiments illustrate that the proposed model deforms ODFs correctly and is capable of handling the classic complex challenges in DWI-registrations, such as the registration of fiber-crossings along with kissing, fanning and interleaving fibers. Our results clearly illustrate a novel promising regularizing effect, that comes from the nonlinear orientation-based cost function. We illustrate the properties of the different image scales, and show that including orientational information in our model make the model better at retrieving deformations compared to standard scalar-based registration.
Image registration refers to a process that transforms data into a shared coordinate system. For DWI, the common way to register two images is to use scalar-based methods on quantitative measures, such as the fractional anisotropy (FA) or the mean diffusivity (MD) @cite_27 . However, as such methods disregard most of the directional information in DWI, methods have been developed to also account for the reorientation of the diffusion profile. Most of these are created on top of scalar-based methods and iteratively reorients the gradients after changing the deformation field. Some of the most popular methods can be found in @cite_19 @cite_5 @cite_26 @cite_29 . However, registration frameworks have also been designed with an objective function that explicitly optimizes over the reorientation of the gradients, such as DTI-TK @cite_15 , DT-REFineD @cite_23 , and the more recent DR-TAMAS @cite_18 . These frameworks have been shown to generally outperform scalar-based frameworks for DWI @cite_14 @cite_13 @cite_35 @cite_25 .
@cite_35 @cite_18 @cite_26 @cite_14 @cite_29 @cite_19 @cite_27 @cite_23 @cite_5 @cite_15 @cite_13 @cite_25
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Abstract Registration plays an important role in group analysis of diffusion-weighted imaging (DWI) data. It can be used to build a reference anatomy for investigating structural variation or tracking changes in white matter. Unlike traditional scalar image registration where spatial alignment is the only focus, registration of DWI data requires both spatial alignment of structures and reorientation of local signal profiles. As such, DWI registration is much more complex and challenging than scalar image registration. Although a variety of algorithms has been proposed to tackle the problem, most of them are restricted by the diffusion model used for registration, making it difficult to fit to the registered data a different model. In this paper we describe a method that allows any diffusion model to be fitted after registration for subsequent multifaceted analysis. This is achieved by directly aligning DWI data using a large deformation diffeomorphic registration framework. Our algorithm seeks the optimal coordinate mapping by simultaneously considering structural alignment, local signal profile reorientation, and deformation regularization. Our algorithm also incorporates a multi-kernel strategy to concurrently register anatomical structures at different scales. We demonstrate the efficacy of our approach using in vivo data and report detailed qualitative and quantitative results in comparison with several different registration strategies. Registration is a prerequisite for fusion of geometrically distorted images. Traditionally, intensity-based image registration methods are preferred to feature-based ones due to higher accuracy of the former than that of the latter. To reduce computational load, image registration is often carried out using the approximate-level coefficients of a wavelet-like transform. Directional selectivity of the transform and the objective function used for the coefficients play vital roles in the alignment process of images. This paper introduces an image registration algorithm that uses the approximate-level coefficients of the curvelet transform, directional selectivity of which is better than many wavelet-like transforms. A conditional entropy-based objective function is developed for registration using a suitable probabilistic model of the curvelet coefficients of images. Suitability of the probability distribution of the coefficients is validated using a standard method to assess goodness of fit. To align the distorted images, the affine transformation that possesses parameters related to the translation, rotation, scaling, and shearing is used. Extensive experimentations are carried out to test the performance of the proposed registration method considering that the images are synthetically or naturally distorted. Experimental results show that performance of the proposed registration method is superior to existing methods in terms of commonly used performance metrics. Image registration is the process of establishing a common geometric reference frame between two or more image data sets possibly taken at different times. In this paper we present a method for computing elastic registration and warping maps based on the Monge–Kantorovich theory of optimal mass transport. This mass transport method has a number of important characteristics. First, it is parameter free. Moreover, it utilizes all of the grayscale data in both images, places the two images on equal footing and is symmetrical: the optimal mapping from image A to image B being the inverse of the optimal mapping from B to A. The method does not require that landmarks be specified, and the minimizer of the distance functional involved is uniques there are no other local minimizers. Finally, optimal transport naturally takes into account changes in density that result from changes in area or volume. Although the optimal transport method is certainly not appropriate for all registration and warping problems, this mass preservation property makes the Monge–Kantorovich approach quite useful for an interesting class of warping problems, as we show in this paper. Our method for finding the registration mapping is based on a partial differential equation approach to the minimization of the L2 Kantorovich–Wasserstein or “Earth Mover's Distance” under a mass preservation constraint. We show how this approach leads to practical algorithms, and demonstrate our method with a number of examples, including those from the medical field. We also extend this method to take into account changes in intensity, and show that it is well suited for applications such as image morphing. In this paper, we propose the DT-REFinD algorithm for the diffeomorphic nonlinear registration of diffusion tensor images. Unlike scalar images, deforming tensor images requires choosing both a reorientation strategy and an interpolation scheme. Current diffusion tensor registration algorithms that use full tensor information face difficulties in computing the differential of the tensor reorientation strategy and consequently, these methods often approximate the gradient of the objective function. In the case of the finite-strain (FS) reorientation strategy, we borrow results from the pose estimation literature in computer vision to derive an analytical gradient of the registration objective function. By utilizing the closed-form gradient and the velocity field representation of one parameter subgroups of diffeomorphisms, the resulting registration algorithm is diffeomorphic and fast. We contrast the algorithm with a traditional FS alternative that ignores the reorientation in the gradient computation. We show that the exact gradient leads to significantly better registration at the cost of computation time. Independently of the choice of Euclidean or Log-Euclidean interpolation and sum of squared differences dissimilarity measure, the exact gradient achieves better alignment over an entire spectrum of deformation penalties. Alignment quality is assessed with a battery of metrics including tensor overlap, fractional anisotropy, inverse consistency and closeness to synthetic warps. The improvements persist even when a different reorientation scheme, preservation of principal directions, is used to apply the final deformations. We present a method for fast, approximate registration of whole-slide images (WSIs) of histopathology serial sections. Popular histopathology slide registration methods in the existing literature tend towards intensity-based approaches. 1, 2 Further input, in the form of an approximate initial transformation to be applied to one of the two WSIs, is then usually required, and this transformation needs to be optimised. Such a transformation is not readily available in this context and thus there is a need for fast approximation of these parameters. Fast registration is achieved by comparison of the external boundaries of adjacent tissue sections, using local curvature on multiple scales to assess similarity. Our representation of curvature is a modified version of the Curvature Scale Space (CSS) 3 image. We substitute zero crossings with signed local absolute maxima of curvature to improve the registration's robustness to the subtle morphological differences of adjacent sections. A pairwise matching is made between curvature maxima at scales increasing exponentially, the matching minimizes the distance between maxima pairs at each scale. The boundary points corresponding to the matched maxima pairs are used to estimate the desired transformation. Our method is highly robust to translation, rotation, and linear scaling, and shows good performance in cases of moderate non-linear scaling. On our set of test images the algorithm shows improved reliability and processing speed in comparison to existing CSS based registration methods. We present a framework for robustly estimating registration between a 3D volume image and a 2D projection image and evaluate its precision and robustness in spine interventions for vertebral localization in the presence of anatomical deformation. The framework employs a normalized gradient information similarity metric and multi-start covariance matrix adaptation evolution strategy optimization with local-restarts, which provided improved robustness against deformation and content mismatch. The parallelized implementation allowed orders-of-magnitude acceleration in computation time and improved the robustness of registration via multi-start global optimization. Experiments involved a cadaver specimen and two CT datasets (supine and prone) and 36 C-arm fluoroscopy images acquired with the specimen in four positions (supine, prone, supine with lordosis, prone with kyphosis), three regions (thoracic, abdominal, and lumbar), and three levels of geometric magnification (1.7, 2.0, 2.4). Registration accuracy was evaluated in terms of projection distance error (PDE) between the estimated and true target points in the projection image, including 14 400 random trials (200 trials on the 72 registration scenarios) with initialization error up to ±200 mm and ±10°. The resulting median PDE was better than 0.1 mm in all cases, depending somewhat on the resolution of input CT and fluoroscopy images. The cadaver experiments illustrated the tradeoff between robustness and computation time, yielding a success rate of 99.993 in vertebral labeling (with 'success' defined as PDE <5 mm) using 1,718 664 ± 96 582 function evaluations computed in 54.0 ± 3.5 s on a mid-range GPU (nVidia, GeForce GTX690). Parameters yielding a faster search (e.g., fewer multi-starts) reduced robustness under conditions of large deformation and poor initialization (99.535 success for the same data registered in 13.1 s), but given good initialization (e.g., ±5 mm, assuming a robust initial run) the same registration could be solved with 99.993 success in 6.3 s. The ability to register CT to fluoroscopy in a manner robust to patient deformation could be valuable in applications such as radiation therapy, interventional radiology, and an assistant to target localization (e.g., vertebral labeling) in image-guided spine surgery. Image registration, the process of aligning two or more images, is the core technique of many (semi-)automatic medical image analysis tasks. Recent studies have shown that deep learning methods, notably convolutional neural networks (ConvNets), can be used for image registration. Thus far training of ConvNets for registration was supervised using predefined example registrations. However, obtaining example registrations is not trivial. To circumvent the need for predefined examples, and thereby to increase convenience of training ConvNets for image registration, we propose the Deep Learning Image Registration (DLIR) framework for unsupervised affine and deformable image registration. In the DLIR framework ConvNets are trained for image registration by exploiting image similarity analogous to conventional intensity-based image registration. After a ConvNet has been trained with the DLIR framework, it can be used to register pairs of unseen images in one shot. We propose flexible ConvNets designs for affine image registration and for deformable image registration. By stacking multiple of these ConvNets into a larger architecture, we are able to perform coarse-to-fine image registration. We show for registration of cardiac cine MRI and registration of chest CT that performance of the DLIR framework is comparable to conventional image registration while being several orders of magnitude faster. In this work, we propose DR-TAMAS (Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures), a novel framework for intersubject registration of Diffusion Tensor Imaging (DTI) data sets. This framework is optimized for brain data and its main goal is to achieve an accurate alignment of all brain structures, including white matter (WM), gray matter (GM), and spaces containing cerebrospinal fluid (CSF). Currently most DTI-based spatial normalization algorithms emphasize alignment of anisotropic structures. While some diffusion-derived metrics, such as diffusion anisotropy and tensor eigenvector orientation, are highly informative for proper alignment of WM, other tensor metrics such as the trace or mean diffusivity (MD) are fundamental for a proper alignment of GM and CSF boundaries. Moreover, it is desirable to include information from structural MRI data, e.g., T1-weighted or T2-weighted images, which are usually available together with the diffusion data. The fundamental property of DR-TAMAS is to achieve global anatomical accuracy by incorporating in its cost function the most informative metrics locally. Another important feature of DR-TAMAS is a symmetric time-varying velocity-based transformation model, which enables it to account for potentially large anatomical variability in healthy subjects and patients. The performance of DR-TAMAS is evaluated with several data sets and compared with other widely-used diffeomorphic image registration techniques employing both full tensor information and or DTI-derived scalar maps. Our results show that the proposed method has excellent overall performance in the entire brain, while being equivalent to the best existing methods in WM. Deformable image registration is a fundamental task in medical image analysis, aiming to establish a dense and non-linear correspondence between a pair of images. Previous deep-learning studies usually employ supervised neural networks to directly learn the spatial transformation from one image to another, requiring task-specific ground-truth registration for model training. Due to the difficulty in collecting precise ground-truth registration, implementation of these supervised methods is practically challenging. Although several unsupervised networks have been recently developed, these methods usually ignore the inherent inverse-consistent property (essential for diffeomorphic mapping) of transformations between a pair of images. Also, existing approaches usually encourage the to-be-estimated transformation to be locally smooth via a smoothness constraint only, which could not completely avoid folding in the resulting transformation. To this end, we propose an Inverse-Consistent deep Network (ICNet) for unsupervised deformable image registration. Specifically, we develop an inverse-consistent constraint to encourage that a pair of images are symmetrically deformed toward one another, until both warped images are matched. Besides using the conventional smoothness constraint, we also propose an anti-folding constraint to further avoid folding in the transformation. The proposed method does not require any supervision information, while encouraging the diffeomoprhic property of the transformation via the proposed inverse-consistent and anti-folding constraints. We evaluate our method on T1-weighted brain magnetic resonance imaging (MRI) scans for tissue segmentation and anatomical landmark detection, with results demonstrating the superior performance of our ICNet over several state-of-the-art approaches for deformable image registration. Our code will be made publicly available. In this paper, we introduce a novel and efficient approach to dense image registration, which does not require a derivative of the employed cost function. In such a context, the registration problem is formulated using a discrete Markov random field objective function. First, towards dimensionality reduction on the variables we assume that the dense deformation field can be expressed using a small number of control points (registration grid) and an interpolation strategy. Then, the registration cost is expressed using a discrete sum over image costs (using an arbitrary similarity measure) projected on the control points, and a smoothness term that penalizes local deviations on the deformation field according to a neighborhood system on the grid. Towards a discrete approach, the search space is quantized resulting in a fully discrete model. In order to account for large deformations and produce results on a high resolution level, a multi-scale incremental approach is considered where the optimal solution is iteratively updated. This is done through successive morphings of the source towards the target image. Efficient linear programming using the primal dual principles is considered to recover the lowest potential of the cost function. Very promising results using synthetic data with known deformations and real data demonstrate the potentials of our approach. Image registration finds a variety of applications in computer vision. Unfortunately, traditional image registration techniques tend to be costly. We present a new image registration technique that makes use of the spatial intensity gradient of the images to find a good match using a type of Newton-Raphson iteration. Our technique is taster because it examines far fewer potential matches between the images than existing techniques Furthermore, this registration technique can be generalized to handle rotation, scaling and shearing. We show how our technique can be adapted tor use in a stereo vision system. Many existing approaches for image-to-geometry registration assume that either a textured 3D model or a good initial guess of the 3D pose is available to bootstrap the registration process. In this paper we consider the registration of photographs to 3D models even when no texture information is available. This is very challenging as we cannot rely on texture gradients, and even shading gradients are hard to estimate since the lighting conditions are unknown. To that end, we propose average shading gradients, a rendering technique that estimates the average gradient magnitude over all lighting directions under Lambertian shading. We use this gradient representation as the building block of a registration pipeline based on matching sparse features. To cope with inevitable false matches due to the missing texture information and to increase robustness, the pose of the 3D model is estimated in two stages. Coarse pose hypotheses are first obtained from a single correct match each, subsequently refined using SIFT flow, and finally verified. We apply our algorithm to registering images of real-world objects to untextured 3D meshes of limited accuracy. Moreover, we show that registration can be performed even for paintings despite lacking photo-realism. With the application in many neuroimaging studies, diffusion tensor image (DTI) registration has generated considerable interest and been studied widely. Although a number of DTI registration methods have been developed, their performances have not yet been compared systematically. This work addresses this gap by comparing a large number of existing DTI registration methods and gives the comprehensive evaluation results. In this paper, the open-access IXI DTI dataset were used. In order to compare the accuracy of tensor matching, 11 open-source registration methods were evaluated with 7 quantitative and open-access evaluation criteria that measure the similarity among tensors (namely tensor-based techniques) or scalar images derived from diffusion tensors (namely scalar-based techniques). The evaluation results indicate that the diffeomorphic deformable tensor registration method (referred to as DTI-TK) is the best method, followed by the symmetric image normalization method (referred to as SyN). Robust image registration in medical imaging is essential for comparison or fusion of images, acquired from various perspectives, modalities or at different times. Typically, an objective function needs to be minimized assuming specific a priori deformation models and predefined or learned similarity measures. However, these approaches have difficulties to cope with large deformations or a large variability in appearance. Using modern deep learning (DL) methods with automated feature design, these limitations could be resolved by learning the intrinsic mapping solely from experience. We investigate in this paper how DL could help organ-specific (ROI-specific) deformable registration, to solve motion compensation or atlas-based segmentation problems for instance in prostate diagnosis. An artificial agent is trained to solve the task of non-rigid registration by exploring the parametric space of a statistical deformation model built from training data. Since it is difficult to extract trustworthy ground-truth deformation fields, we present a training scheme with a large number of synthetically deformed image pairs requiring only a small number of real inter-subject pairs. Our approach was tested on inter-subject registration of prostate MR data and reached a median DICE score of .88 in 2-D and .76 in 3-D, therefore showing improved results compared to state-of-the-art registration algorithms. Conventional approaches to image registration consist of time consuming iterative methods. Most current deep learning (DL) based registration methods extract deep features to use in an iterative setting. We propose an end-to-end DL method for registering multimodal images. Our approach uses generative adversarial networks (GANs) that eliminates the need for time consuming iterative methods, and directly generates the registered image with the deformation field. Appropriate constraints in the GAN cost function produce accurately registered images in less than a second. Experiments demonstrate their accuracy for multimodal retinal and cardiac MR image registration. Many existing approaches for image-to-geometry registration assume that either a textured 3D model or a good initial guess of the 3D pose is available to bootstrap the registration process. In this paper we consider the registration of photographs to 3D models even when no texture information is available. This is very challenging as we cannot rely on texture gradients, and even shading gradients are hard to estimate since the lighting conditions are unknown. To that end, we propose average shading gradients, a rendering technique that estimates the average gradient magnitude over all lighting directions under Lambertian shading. We use this gradient representation as the building block of a registration pipeline based on matching sparse features. To cope with inevitable false matches due to the missing texture information and to increase robustness, the pose of the 3D model is estimated in two stages. Coarse pose hypotheses are first obtained from a single correct match each, subsequently refined using SIFT flow, and finally verified. We apply our algorithm to registering images of real-world objects to untextured 3D meshes of limited accuracy. We propose a novel non-rigid image registration algorithm that is built upon fully convolutional networks (FCNs) to optimize and learn spatial transformations between pairs of images to be registered. Different from most existing deep learning based image registration methods that learn spatial transformations from training data with known corresponding spatial transformations, our method directly estimates spatial transformations between pairs of images by maximizing an image-wise similarity metric between fixed and deformed moving images, similar to conventional image registration algorithms. At the same time, our method also learns FCNs for encoding the spatial transformations at the same spatial resolution of images to be registered, rather than learning coarse-grained spatial transformation information. The image registration is implemented in a multi-resolution image registration framework to jointly optimize and learn spatial transformations and FCNs at different resolutions with deep self-supervision through typical feedforward and backpropagation computation. Since our method simultaneously optimizes and learns spatial transformations for the image registration, our method can be directly used to register a pair of images, and the registration of a set of images is also a training procedure for FCNs so that the trained FCNs can be directly adopted to register new images by feedforward computation of the learned FCNs without any optimization. The proposed method has been evaluated for registering 3D structural brain magnetic resonance (MR) images and obtained better performance than state-of-the-art image registration algorithms. In this paper, we present a novel deformable registration algorithm for diffusion tensor MR images that enables explicit optimization of tensor reorientation. The optimization seeks a piecewise affine transformation that divides the image domain into uniform regions and transform each region affinely. The objective function captures both the image similarity and the smoothness of the transformation across region boundaries. The image similarity enables explicit orientation optimization by incorporating tensor reorientation, which is necessary for warping diffusion tensor images. The objective function is formulated in a way that allows explicit implementation of analytic derivatives to drive fast and accurate optimization using the conjugate gradient method. By explicitly optimizing tensor reorientation, the algorithm is designed to take advantage of similarity measures comparing tensors as a whole. The optimal transformation is hierarchically refined in a subdivision framework. A comparison with affine registration for inter-subject normalization of 8 subjects shows that the proposed algorithm improves the alignment of several major white matter structures examined: the anterior thalamic radiations, the inferior fronto-occipital fasciculi, the corticospinal corticobulbar tracts and the genu and the splenium of the corpus callosum. The alignment of white matter structures is assessed using a novel scheme of computing distances between the corresponding fiber bundles derived from tractography. We present a fast learning-based algorithm for deformable, pairwise 3D medical image registration. Current registration methods optimize an objective function independently for each pair of images, which can be time-consuming for large data. We define registration as a parametric function, and optimize its parameters given a set of images from a collection of interest. Given a new pair of scans, we can quickly compute a registration field by directly evaluating the function using the learned parameters. We model this function using a CNN, and use a spatial transform layer to reconstruct one image from another while imposing smoothness constraints on the registration field. The proposed method does not require supervised information such as ground truth registration fields or anatomical landmarks. We demonstrate registration accuracy comparable to state-of-the-art 3D image registration, while operating orders of magnitude faster in practice. Our method promises to significantly speed up medical image analysis and processing pipelines, while facilitating novel directions in learning-based registration and its applications. Our code is available at https: github.com balakg voxelmorph. Robust image registration is a challenging problem, especially when dealing with severe changes in illumination and viewpoint. Previous methods assume a global geometric model (e.g., homography) and, hence, are only able to align images under predefined constraints (e.g., planar scenes and parallax-free camera motion). However, these constraints may not hold for natural scenes and uncontrolled imaging conditions. Therefore, this paper proposes a novel method which approximates image regions with planes by incorporating piecewise local geometric models. The approximated planar regions are obtained by exploiting a hierarchical figure-ground segmentation method. Each such planar region assumes an affine transformation. To achieve the alignment of the planar regions, an energy function is defined which employs intensity, a key-point descriptor, and geometric information under a global constraint. By re-segmenting and re-merging planar regions iteratively in an energy minimization framework, the method is able to align images even under significant changes in illumination and viewpoint. Experiments on two datasets show that the proposed method outperforms state-of-the-art, especially in the case of large appearance variations and it is, therefore, applicable to web-images (i.e., unconstrained setting) which are taken from the same scene with different viewpoints.