We present recursive cascaded networks, a general architecture that enables learning deep cascades, for deformable image registration. The proposed architecture is simple in design and can be built on any base network. The moving image is warped successively by each cascade and finally aligned to the fixed image; this procedure is recursive in a way that every cascade learns to perform a progressive deformation for the current warped image. The entire system is end-to-end and jointly trained in an unsupervised manner. In addition, enabled by the recursive architecture, one cascade can be iteratively applied for multiple times during testing, which approaches a better fit between each of the image pairs. We evaluate our method on 3D medical images, where deformable registration is most commonly applied. We demonstrate that recursive cascaded networks achieve consistent, significant gains and outperform state-of-the-art methods. The performance reveals an increasing trend as long as more cascades are trained, while the limit is not observed. Our code will be made publicly available.
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. 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. We present VoxelMorph, a fast learning-based framework for deformable, pairwise medical image registration. Traditional registration methods optimize an objective function for each pair of images, which can be time-consuming for large datasets or rich deformation models. In contrast to this approach and building on recent learning-based methods, we formulate registration as a function that maps an input image pair to a deformation field that aligns these images. We parameterize the function via a convolutional neural network and optimize the parameters of the neural network on a set of images. Given a new pair of scans, VoxelMorph rapidly computes a deformation field by directly evaluating the function. In this paper, we explore two different training strategies. In the first (unsupervised) setting, we train the model to maximize standard image matching objective functions that are based on the image intensities. In the second setting, we leverage auxiliary segmentations available in the training data. We demonstrate that the unsupervised model’s accuracy is comparable to the state-of-the-art methods while operating orders of magnitude faster. We also show that VoxelMorph trained with auxiliary data improves registration accuracy at test time and evaluate the effect of training set size on registration. Our method promises to speed up medical image analysis and processing pipelines while facilitating novel directions in learning-based registration and its applications. Our code is freely available at https: github.com voxelmorph voxelmorph . Existing deformable registration methods require exhaustively iterative optimization, along with careful parameter tuning, to estimate the deformation field between images. Although some learning-based methods have been proposed for initiating deformation estimation, they are often template-specific and not flexible in practical use. In this paper, we propose a convolutional neural network (CNN) based regression model to directly learn the complex mapping from the input image pair (i.e., a pair of template and subject) to their corresponding deformation field. Specifically, our CNN architecture is designed in a patch-based manner to learn the complex mapping from the input patch pairs to their respective deformation field. First, the equalized active-points guided sampling strategy is introduced to facilitate accurate CNN model learning upon a limited image dataset. Then, the similarity-steered CNN architecture is designed, where we propose to add the auxiliary contextual cue, i.e., the similarity between input patches, to more directly guide the learning process. Experiments on different brain image datasets demonstrate promising registration performance based on our CNN model. Furthermore, it is found that the trained CNN model from one dataset can be successfully transferred to another dataset, although brain appearances across datasets are quite variable. In this paper we present SimpleElastix, an extension of SimpleITK designed to bring the Elastix medical image registration library to a wider audience. Elastix is a modular collection of robust C++ image registration algorithms that is widely used in the literature. However, its command-line interface introduces overhead during prototyping, experimental setup, and tuning of registration algorithms. By integrating Elastix with SimpleITK, Elastix can be used as a native library in Python, Java, R, Octave, Ruby, Lua, Tcl and C# on Linux, Mac and Windows. This allows Elastix to intregrate naturally with many development environments so the user can focus more on the registration problem and less on the underlying C++ implementation. As means of demonstration, we show how to register MR images of brains and natural pictures of faces using minimal amount of code. SimpleElastix is open source, licensed under the permissive Apache License Version 2.0 and available at https: github.com kaspermarstal SimpleElastix. 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. We propose a novel semantic segmentation algorithm by learning a deep deconvolution network. We learn the network on top of the convolutional layers adopted from VGG 16-layer net. The deconvolution network is composed of deconvolution and unpooling layers, which identify pixelwise class labels and predict segmentation masks. We apply the trained network to each proposal in an input image, and construct the final semantic segmentation map by combining the results from all proposals in a simple manner. The proposed algorithm mitigates the limitations of the existing methods based on fully convolutional networks by integrating deep deconvolution network and proposal-wise prediction, our segmentation method typically identifies detailed structures and handles objects in multiple scales naturally. Our network demonstrates outstanding performance in PASCAL VOC 2012 dataset, and we achieve the best accuracy (72.5 ) among the methods trained without using Microsoft COCO dataset through ensemble with the fully convolutional network. 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. In this paper we propose a method to solve nonrigid image registration through a learning approach, instead of via iterative optimization of a predefined dissimilarity metric. We design a Convolutional Neural Network (CNN) architecture that, in contrast to all other work, directly estimates the displacement vector field (DVF) from a pair of input images. The proposed RegNet is trained using a large set of artificially generated DVFs, does not explicitly define a dissimilarity metric, and integrates image content at multiple scales to equip the network with contextual information. At testing time nonrigid registration is performed in a single shot, in contrast to current iterative methods. We tested RegNet on 3D chest CT follow-up data. The results show that the accuracy of RegNet is on par with a conventional B-spline registration, for anatomy within the capture range. Training RegNet with artificially generated DVFs is therefore a promising approach for obtaining good results on real clinical data, thereby greatly simplifying the training problem. Deformable image registration can therefore be successfully casted as a learning problem. In this work we propose a deep learning network for deformable image registration (DIRNet). The DIRNet consists of a convolutional neural network (ConvNet) regressor, a spatial transformer, and a resampler. The ConvNet analyzes a pair of fixed and moving images and outputs parameters for the spatial transformer, which generates the displacement vector field that enables the resampler to warp the moving image to the fixed image. The DIRNet is trained end-to-end by unsupervised optimization of a similarity metric between input image pairs. A trained DIRNet can be applied to perform registration on unseen image pairs in one pass, thus non-iteratively. Evaluation was performed with registration of images of handwritten digits (MNIST) and cardiac cine MR scans (Sunnybrook Cardiac Data). The results demonstrate that registration with DIRNet is as accurate as a conventional deformable image registration method with short execution times. Medical image registration is an important task in medical image processing. It refers to the process of aligning data sets, possibly from different modalities (e.g., magnetic resonance and computed tomography), different time points (e.g., follow-up scans), and or different subjects (in case of population studies). A large number of methods for image registration are described in the literature. Unfortunately, there is not one method that works for all applications. We have therefore developed elastix, a publicly available computer program for intensity-based medical image registration. The software consists of a collection of algorithms that are commonly used to solve medical image registration problems. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. The command-line interface enables automated processing of large numbers of data sets, by means of scripting. The usage of elastix for comparing different registration methods is illustrated with three example experiments, in which individual components of the registration method are varied. Deformable image registration (DIR) in thoracic 4D CT image data is integral for, e.g., radiotherapy treatment planning, but time consuming. Deep learning (DL)-based DIR promises speed-up, but present solutions are limited to small image sizes. In this paper, we propose a General Deep Learning-based Fast Image Registration framework suitable for application to clinical 4D CT data (GDL-FIRE (^ 4D )). Open source DIR frameworks are selected to build GDL-FIRE (^ 4D ) variants. In-house-acquired 4D CT images serve as training and open 4D CT data repositories as external evaluation cohorts. Taking up current attempts to DIR uncertainty estimation, dropout-based uncertainty maps for GDL-FIRE (^ 4D ) variants are analyzed. We show that (1) registration accuracy of GDL-FIRE (^ 4D ) and standard DIR are in the same order; (2) computation time is reduced to a few seconds (here: 60-fold speed-up); and (3) dropout-based uncertainty maps do not correlate to across-DIR vector field differences, raising doubts about applicability in the given context. Abstract This paper introduces Quicksilver, a fast deformable image registration method. Quicksilver registration for image-pairs works by patch-wise prediction of a deformation model based directly on image appearance. A deep encoder-decoder network is used as the prediction model. While the prediction strategy is general, we focus on predictions for the Large Deformation Diffeomorphic Metric Mapping (LDDMM) model. Specifically, we predict the momentum-parameterization of LDDMM, which facilitates a patch-wise prediction strategy while maintaining the theoretical properties of LDDMM, such as guaranteed diffeomorphic mappings for sufficiently strong regularization. We also provide a probabilistic version of our prediction network which can be sampled during the testing time to calculate uncertainties in the predicted deformations. Finally, we introduce a new correction network which greatly increases the prediction accuracy of an already existing prediction network. We show experimental results for uni-modal atlas-to-image as well as uni- multi-modal image-to-image registrations. These experiments demonstrate that our method accurately predicts registrations obtained by numerical optimization, is very fast, achieves state-of-the-art registration results on four standard validation datasets, and can jointly learn an image similarity measure. Quicksilver is freely available as an open-source software. 3D medical image registration is of great clinical importance. However, supervised learning methods require a large amount of accurately annotated corresponding control points (or morphing). The ground truth for 3D medical images is very difficult to obtain. Unsupervised learning methods ease the burden of manual annotation by exploiting unlabeled data without supervision. In this paper, we propose a new unsupervised learning method using convolutional neural networks under an end-to-end framework, Volume Tweening Network (VTN), to register 3D medical images. Three technical components ameliorate our unsupervised learning system for 3D end-to-end medical image registration: (1) We cascade the registration subnetworks; (2) We integrate affine registration into our network; and (3) We incorporate an additional invertibility loss into the training process. Experimental results demonstrate that our algorithm is 880x faster (or 3.3x faster without GPU acceleration) than traditional optimization-based methods and achieves state-of-the-art performance in medical image registration.