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Register a new userIntroduction to Medical Image Registration with DeepReg, Between Old and New
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This document outlines a tutorial to get started with medical image registration using the open-source package DeepReg. The basic concepts of medical image registration are discussed, linking classical methods to newer methods using deep learning. Two iterative, classical algorithms using optimisation and one learning-based algorithm using deep learning are coded step-by-step using DeepReg utilities, all with real, open-accessible, medical data.
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DeepReg (https://github.com/DeepRegNet/DeepReg) is a community-supported open-source toolkit for research and education in medical image registration using deep learning.
In the last decade, convolutional neural networks (ConvNets) have dominated and achieved state-of-the-art performances in a variety of medical imaging applications. However, the performances of ConvNets are still limited by lacking the understanding of long-range spatial relations in an image. The recently proposed Vision Transformer (ViT) for image classification uses a purely self-attention-based model that learns long-range spatial relations to focus on the relevant parts of an image. Nevertheless, ViT emphasizes the low-resolution features because of the consecutive downsamplings, result in a lack of detailed localization information, making it unsuitable for image registration. Recently, several ViT-based image segmentation methods have been combined with ConvNets to improve the recovery of detailed localization information. Inspired by them, we present ViT-V-Net, which bridges ViT and ConvNet to provide volumetric medical image registration. The experimental results presented here demonstrate that the proposed architecture achieves superior performance to several top-performing registration methods.
The implementation of medical AI has always been a problem. The effect of traditional perceptual AI algorithm in medical image processing needs to be improved. Here we propose a method of knowledge AI, which is a combination of perceptual AI and clinical knowledge and experience. Based on this method, the geometric information mining of medical images can represent the experience and information and evaluate the quality of medical images.
Medical images such as 3D computerized tomography (CT) scans and pathology images, have hundreds of millions or billions of voxels/pixels. It is infeasible to train CNN models directly on such high resolution images, because neural activations of a single image do not fit in the memory of a single GPU/TPU, and naive data and model parallelism approaches do not work. Existing image analysis approaches alleviate this problem by cropping or down-sampling input images, which leads to complicated implementation and sub-optimal performance due to information loss. In this paper, we implement spatial partitioning, which internally distributes the input and output of convolutional layers across GPUs/TPUs. Our implementation is based on the Mesh-TensorFlow framework and the computation distribution is transparent to end users. With this technique, we train a 3D Unet on up to 512 by 512 by 512 resolution data. To the best of our knowledge, this is the first work for handling such high resolution images end-to-end.
Classical pairwise image registration methods search for a spatial transformation that optimises a numerical measure that indicates how well a pair of moving and fixed images are aligned. Current learning-based registration methods have adopted the same paradigm and typically predict, for any new input image pair, dense correspondences in the form of a dense displacement field or parameters of a spatial transformation model. However, in many applications of registration, the spatial transformation itself is only required to propagate points or regions of interest (ROIs). In such cases, detailed pixel- or voxel-level correspondence within or outside of these ROIs often have little clinical value. In this paper, we propose an alternative paradigm in which the location of corresponding image-specific ROIs, defined in one image, within another image is learnt. This results in replacing image registration by a conditional segmentation algorithm, which can build on typical image segmentation networks and their widely-adopted training strategies. Using the registration of 3D MRI and ultrasound images of the prostate as an example to demonstrate this new approach, we report a median target registration error (TRE) of 2.1 mm between the ground-truth ROIs defined on intraoperative ultrasound images and those propagated from the preoperative MR images. Significantly lower (>34%) TREs were obtained using the proposed conditional segmentation compared with those obtained from a previously-proposed spatial-transformation-predicting registration network trained with the same multiple ROI labels for individual image pairs. We conclude this work by using a quantitative bias-variance analysis to provide one explanation of the observed improvement in registration accuracy.
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