Learning Rigid Image Registration - Utilizing Convolutional Neural Networks for Medical Image Registration

Many traditional computer vision tasks, such as segmentation, have seen large step-changes in accuracy and/or speed with the application of Convolutional Neural Networks (CNNs). Image registration, the alignment of two or more images to a common space, is a fundamental step in many medical imaging workflows. In this paper we investigate whether these techniques can also bring tangible benefits to the registration task. We describe and evaluate the use of convolutional neural networks (CNNs) for both mono- and multi- modality registration and compare their performance to more traditional schemes, namely multi-scale, iterative registration. This paper also investigates incorporating inverse consistency of the learned spatial transformations to impose additional constraints on the network during training and investigate any benefit in accuracy during detection. The approaches are validated with a series of artificial mono-modal registration tasks utilizing T1-weighted MR brain i mages from the Open Access Series of Imaging Studies (OASIS) study and IXI brain development dataset and a series of real multi-modality registration tasks using T1-weighted and T2-weighted MR brain images from the 2015 Ischemia Stroke Lesion segmentation (ISLES) challenge. The results demonstrate that CNNs give excellent performance for both mono- and multi- modality head and neck registration compared to the baseline method with significantly fewer outliers and lower mean errors

Learning Deep Similarity Metric for 3D MR-TRUS Registration

Purpose: The fusion of transrectal ultrasound (TRUS) and magnetic resonance (MR) images for guiding targeted prostate biopsy has significantly improved the biopsy yield of aggressive cancers. A key component of MR-TRUS fusion is image registration. However, it is very challenging to obtain a robust automatic MR-TRUS registration due to the large appearance difference between the two imaging modalities. The work presented in this paper aims to tackle this problem by addressing two challenges: (i) the definition of a suitable similarity metric and (ii) the determination of a suitable optimization strategy. Methods: This work proposes the use of a deep convolutional neural network to learn a similarity metric for MR-TRUS registration. We also use a composite optimization strategy that explores the solution space in order to search for a suitable initialization for the second-order optimization of the learned metric. Further, a multi-pass approach is used in order to smooth the metric for optimization. Results: The learned similarity metric outperforms the classical mutual information and also the state-of-the-art MIND feature based methods. The results indicate that the overall registration framework has a large capture range. The proposed deep similarity metric based approach obtained a mean TRE of 3.86mm (with an initial TRE of 16mm) for this challenging problem. Conclusion: A similarity metric that is learned using a deep neural network can be used to assess the quality of any given image registration and can be used in conjunction with the aforementioned optimization framework to perform automatic registration that is robust to poor initialization.Comment: To appear on IJCAR

Deeply-Supervised CNN for Prostate Segmentation

Prostate segmentation from Magnetic Resonance (MR) images plays an important role in image guided interven- tion. However, the lack of clear boundary specifically at the apex and base, and huge variation of shape and texture between the images from different patients make the task very challenging. To overcome these problems, in this paper, we propose a deeply supervised convolutional neural network (CNN) utilizing the convolutional information to accurately segment the prostate from MR images. The proposed model can effectively detect the prostate region with additional deeply supervised layers compared with other approaches. Since some information will be abandoned after convolution, it is necessary to pass the features extracted from early stages to later stages. The experimental results show that significant segmentation accuracy improvement has been achieved by our proposed method compared to other reported approaches.Comment: Due to a crucial sign error in equation

Adversarial Deformation Regularization for Training Image Registration Neural Networks

We describe an adversarial learning approach to constrain convolutional neural network training for image registration, replacing heuristic smoothness measures of displacement fields often used in these tasks. Using minimally-invasive prostate cancer intervention as an example application, we demonstrate the feasibility of utilizing biomechanical simulations to regularize a weakly-supervised anatomical-label-driven registration network for aligning pre-procedural magnetic resonance (MR) and 3D intra-procedural transrectal ultrasound (TRUS) images. A discriminator network is optimized to distinguish the registration-predicted displacement fields from the motion data simulated by finite element analysis. During training, the registration network simultaneously aims to maximize similarity between anatomical labels that drives image alignment and to minimize an adversarial generator loss that measures divergence between the predicted- and simulated deformation. The end-to-end trained network enables efficient and fully-automated registration that only requires an MR and TRUS image pair as input, without anatomical labels or simulated data during inference. 108 pairs of labelled MR and TRUS images from 76 prostate cancer patients and 71,500 nonlinear finite-element simulations from 143 different patients were used for this study. We show that, with only gland segmentation as training labels, the proposed method can help predict physically plausible deformation without any other smoothness penalty. Based on cross-validation experiments using 834 pairs of independent validation landmarks, the proposed adversarial-regularized registration achieved a target registration error of 6.3 mm that is significantly lower than those from several other regularization methods.Comment: Accepted to MICCAI 201

Dilated FCN for Multi-Agent 2D/3D Medical Image Registration

2D/3D image registration to align a 3D volume and 2D X-ray images is a challenging problem due to its ill-posed nature and various artifacts presented in 2D X-ray images. In this paper, we propose a multi-agent system with an auto attention mechanism for robust and efficient 2D/3D image registration. Specifically, an individual agent is trained with dilated Fully Convolutional Network (FCN) to perform registration in a Markov Decision Process (MDP) by observing a local region, and the final action is then taken based on the proposals from multiple agents and weighted by their corresponding confidence levels. The contributions of this paper are threefold. First, we formulate 2D/3D registration as a MDP with observations, actions, and rewards properly defined with respect to X-ray imaging systems. Second, to handle various artifacts in 2D X-ray images, multiple local agents are employed efficiently via FCN-based structures, and an auto attention mechanism is proposed to favor the proposals from regions with more reliable visual cues. Third, a dilated FCN-based training mechanism is proposed to significantly reduce the Degree of Freedom in the simulation of registration environment, and drastically improve training efficiency by an order of magnitude compared to standard CNN-based training method. We demonstrate that the proposed method achieves high robustness on both spine cone beam Computed Tomography data with a low signal-to-noise ratio and data from minimally invasive spine surgery where severe image artifacts and occlusions are presented due to metal screws and guide wires, outperforming other state-of-the-art methods (single agent-based and optimization-based) by a large margin.Comment: AAAI 201

Deep learning cardiac motion analysis for human survival prediction

Motion analysis is used in computer vision to understand the behaviour of moving objects in sequences of images. Optimising the interpretation of dynamic biological systems requires accurate and precise motion tracking as well as efficient representations of high-dimensional motion trajectories so that these can be used for prediction tasks. Here we use image sequences of the heart, acquired using cardiac magnetic resonance imaging, to create time-resolved three-dimensional segmentations using a fully convolutional network trained on anatomical shape priors. This dense motion model formed the input to a supervised denoising autoencoder (4Dsurvival), which is a hybrid network consisting of an autoencoder that learns a task-specific latent code representation trained on observed outcome data, yielding a latent representation optimised for survival prediction. To handle right-censored survival outcomes, our network used a Cox partial likelihood loss function. In a study of 302 patients the predictive accuracy (quantified by Harrell's C-index) was significantly higher (p < .0001) for our model C=0.73 (95$\%$ CI: 0.68 - 0.78) than the human benchmark of C=0.59 (95$\%$ CI: 0.53 - 0.65). This work demonstrates how a complex computer vision task using high-dimensional medical image data can efficiently predict human survival