Albert C. S. Chung

Tony C. W. Mok, Albert C. S. Chung

Affine registration is indispensable in a comprehensive medical image registration pipeline. However, only a few studies focus on fast and robust affine registration algorithms. Most of these studies utilize convolutional neural networks (CNNs) to learn joint affine and non-parametric registration, while the standalone performance of the affine subnetwork is less explored. Moreover, existing CNN-based affine registration approaches focus either on the local misalignment or the global orientation and position of the input to predict the affine transformation matrix, which are sensitive to spatial initialization and exhibit limited generalizability apart from the training dataset. In this paper, we present a fast and robust learning-based algorithm, Coarse-to-Fine Vision Transformer (C2FViT), for 3D affine medical image registration. Our method naturally leverages the global connectivity and locality of the convolutional vision transformer and the multi-resolution strategy to learn the global affine registration. We evaluate our method on 3D brain atlas registration and template-matching normalization. Comprehensive results demonstrate that our method is superior to the existing CNNs-based affine registration methods in terms of registration accuracy, robustness and generalizability while preserving the runtime advantage of the learning-based methods. The source code is available at https://github.com/cwmok/C2FViT.

Tony C. W. Mok, Albert C. S. Chung

Registration of pre-operative and post-recurrence brain images is often needed to evaluate the effectiveness of brain gliomas treatment. While recent deep learning-based deformable registration methods have achieved remarkable success with healthy brain images, most of them would be unable to accurately align images with pathologies due to the absent correspondences in the reference image. In this paper, we propose a deep learning-based deformable registration method that jointly estimates regions with absent correspondence and bidirectional deformation fields. A forward-backward consistency constraint is used to aid in the localization of the resection and recurrence region from voxels with absence correspondences in the two images. Results on 3D clinical data from the BraTS-Reg challenge demonstrate our method can improve image alignment compared to traditional and deep learning-based registration approaches with or without cost function masking strategy. The source code is available at https://github.com/cwmok/DIRAC.

Tony C. W. Mok, Albert C. S. Chung

Registration of pre-operative and follow-up brain MRI scans is challenging due to the large variation of tissue appearance and missing correspondences in tumour recurrence regions caused by tumour mass effect. Although recent deep learning-based deformable registration methods have achieved remarkable success in various medical applications, most of them are not capable of registering images with pathologies. In this paper, we propose a 3-step registration pipeline for pre-operative and follow-up brain MRI scans that consists of 1) a multi-level affine registration, 2) a conditional deep Laplacian pyramid image registration network (cLapIRN) with forward-backward consistency constraint, and 3) a non-linear instance optimization method. We apply the method to the Brain Tumor Sequence Registration (BraTS-Reg) Challenge. Our method achieves accurate and robust registration of brain MRI scans with pathologies, which achieves a median absolute error of 1.64 mm and 88\% of successful registration rate in the validation set of BraTS-Reg challenge. Our method ranks 1st place in the 2022 MICCAI BraTS-Reg challenge.

Ziyi He, Albert C. S. Chung

Template generation is a critical step in groupwise image registration, which involves aligning a group of subjects into a common space. While existing methods can generate high-quality template images, they often incur substantial time costs or are limited by fixed group scales. In this paper, we present InstantGroup, an efficient groupwise template generation framework based on variational autoencoder (VAE) models that leverage latent representations' arithmetic properties, enabling scalability to groups of any size. InstantGroup features a Dual VAE backbone with shared-weight twin networks to handle pairs of inputs and incorporates a Displacement Inversion Module (DIM) to maintain template unbiasedness and a Subject-Template Alignment Module (STAM) to improve template quality and registration accuracy. Experiments on 3D brain MRI scans from the OASIS and ADNI datasets reveal that InstantGroup dramatically reduces runtime, generating templates within seconds for various group sizes while maintaining superior performance compared to state-of-the-art baselines on quantitative metrics, including unbiasedness and registration accuracy.

Rongzhao Zhang, Han Zhang, Albert C. S. Chung

Automatic mammogram classification and mass segmentation play a critical role in a computer-aided mammogram screening system. In this work, we present a unified mammogram analysis framework for both whole-mammogram classification and segmentation. Our model is designed based on a deep U-Net with residual connections, and equipped with the novel hybrid deep supervision (HDS) scheme for end-to-end multi-task learning. As an extension of deep supervision (DS), HDS not only can force the model to learn more discriminative features like DS, but also seamlessly integrates segmentation and classification tasks into one model, thus the model can benefit from both pixel-wise and image-wise supervisions. We extensively validate the proposed method on the widely-used INbreast dataset. Ablation study corroborates that pixel-wise and image-wise supervisions are mutually beneficial, evidencing the efficacy of HDS. The results of 5-fold cross validation indicate that our unified model matches state-of-the-art performance on both mammogram segmentation and classification tasks, which achieves an average segmentation Dice similarity coefficient (DSC) of 0.85 and a classification accuracy of 0.89. The code is available at https://github.com/angrypudding/hybrid-ds.

Alessa Hering, Lasse Hansen, Tony C. W. Mok et al.

Image registration is a fundamental medical image analysis task, and a wide variety of approaches have been proposed. However, only a few studies have comprehensively compared medical image registration approaches on a wide range of clinically relevant tasks. This limits the development of registration methods, the adoption of research advances into practice, and a fair benchmark across competing approaches. The Learn2Reg challenge addresses these limitations by providing a multi-task medical image registration data set for comprehensive characterisation of deformable registration algorithms. A continuous evaluation will be possible at https://learn2reg.grand-challenge.org. Learn2Reg covers a wide range of anatomies (brain, abdomen, and thorax), modalities (ultrasound, CT, MR), availability of annotations, as well as intra- and inter-patient registration evaluation. We established an easily accessible framework for training and validation of 3D registration methods, which enabled the compilation of results of over 65 individual method submissions from more than 20 unique teams. We used a complementary set of metrics, including robustness, accuracy, plausibility, and runtime, enabling unique insight into the current state-of-the-art of medical image registration. This paper describes datasets, tasks, evaluation methods and results of the challenge, as well as results of further analysis of transferability to new datasets, the importance of label supervision, and resulting bias. While no single approach worked best across all tasks, many methodological aspects could be identified that push the performance of medical image registration to new state-of-the-art performance. Furthermore, we demystified the common belief that conventional registration methods have to be much slower than deep-learning-based methods.

Tony C. W. Mok, Albert C. S. Chung

Recent deep learning-based methods have shown promising results and runtime advantages in deformable image registration. However, analyzing the effects of hyperparameters and searching for optimal regularization parameters prove to be too prohibitive in deep learning-based methods. This is because it involves training a substantial number of separate models with distinct hyperparameter values. In this paper, we propose a conditional image registration method and a new self-supervised learning paradigm for deep deformable image registration. By learning the conditional features that are correlated with the regularization hyperparameter, we demonstrate that optimal solutions with arbitrary hyperparameters can be captured by a single deep convolutional neural network. In addition, the smoothness of the resulting deformation field can be manipulated with arbitrary strength of smoothness regularization during inference. Extensive experiments on a large-scale brain MRI dataset show that our proposed method enables the precise control of the smoothness of the deformation field without sacrificing the runtime advantage or registration accuracy.

Yongxiang Huang, Albert C. S. Chung

There is a rising need for computational models that can complementarily leverage data of different modalities while investigating associations between subjects for population-based disease analysis. Despite the success of convolutional neural networks in representation learning for imaging data, it is still a very challenging task. In this paper, we propose a generalizable framework that can automatically integrate imaging data with non-imaging data in populations for uncertainty-aware disease prediction. At its core is a learnable adaptive population graph with variational edges, which we mathematically prove that it is optimizable in conjunction with graph convolutional neural networks. To estimate the predictive uncertainty related to the graph topology, we propose the novel concept of Monte-Carlo edge dropout. Experimental results on four databases show that our method can consistently and significantly improve the diagnostic accuracy for Autism spectrum disorder, Alzheimer's disease, and ocular diseases, indicating its generalizability in leveraging multimodal data for computer-aided diagnosis.

Tony C. W. Mok, Albert C. S. Chung

Deep learning-based methods have recently demonstrated promising results in deformable image registration for a wide range of medical image analysis tasks. However, existing deep learning-based methods are usually limited to small deformation settings, and desirable properties of the transformation including bijective mapping and topology preservation are often being ignored by these approaches. In this paper, we propose a deep Laplacian Pyramid Image Registration Network, which can solve the image registration optimization problem in a coarse-to-fine fashion within the space of diffeomorphic maps. Extensive quantitative and qualitative evaluations on two MR brain scan datasets show that our method outperforms the existing methods by a significant margin while maintaining desirable diffeomorphic properties and promising registration speed.

Tony C. W. Mok, Albert C. S. Chung

Diffeomorphic deformable image registration is crucial in many medical image studies, as it offers unique, special properties including topology preservation and invertibility of the transformation. Recent deep learning-based deformable image registration methods achieve fast image registration by leveraging a convolutional neural network (CNN) to learn the spatial transformation from the synthetic ground truth or the similarity metric. However, these approaches often ignore the topology preservation of the transformation and the smoothness of the transformation which is enforced by a global smoothing energy function alone. Moreover, deep learning-based approaches often estimate the displacement field directly, which cannot guarantee the existence of the inverse transformation. In this paper, we present a novel, efficient unsupervised symmetric image registration method which maximizes the similarity between images within the space of diffeomorphic maps and estimates both forward and inverse transformations simultaneously. We evaluate our method on 3D image registration with a large scale brain image dataset. Our method achieves state-of-the-art registration accuracy and running time while maintaining desirable diffeomorphic properties.

Zhou He, Siqi Bao, Albert Chung

Recent advancements in medical image segmentation techniques have achieved compelling results. However, most of the widely used approaches do not take into account any prior knowledge about the shape of the biomedical structures being segmented. More recently, some works have presented approaches to incorporate shape information. However, many of them are indeed introducing more parameters to the segmentation network to learn the general features, which any segmentation network is able learn, instead of specifically shape features. In this paper, we present a novel approach that seamlessly integrates the shape information into the segmentation network. Experiments on human brain MRI segmentation demonstrate that our approach can achieve a lower Hausdorff distance and higher Dice coefficient than the state-of-the-art approaches.

Rongzhao Zhang, Albert C. S. Chung

When introducing advanced image computing algorithms, e.g., whole-heart segmentation, into clinical practice, a common suspicion is how reliable the automatically computed results are. In fact, it is important to find out the failure cases and identify the misclassified pixels so that they can be excluded or corrected for the subsequent analysis or diagnosis. However, it is not a trivial problem to predict the errors in a segmentation mask when ground truth (usually annotated by experts) is absent. In this work, we attempt to address the pixel-wise error map prediction problem and the per-case mask quality assessment problem using a unified deep learning (DL) framework. Specifically, we first formalize an error map prediction problem, then we convert it to a segmentation problem and build a DL network to tackle it. We also derive a quality indicator (QI) from a predicted error map to measure the overall quality of a segmentation mask. To evaluate the proposed framework, we perform extensive experiments on a public whole-heart segmentation dataset, i.e., MICCAI 2017 MMWHS. By 5-fold cross validation, we obtain an overall Dice score of 0.626 for the error map prediction task, and observe a high Pearson correlation coefficient (PCC) of 0.972 between QI and the actual segmentation accuracy (Acc), as well as a low mean absolute error (MAE) of 0.0048 between them, which evidences the efficacy of our method in both error map prediction and quality assessment.

Tony C. W Mok, Albert C. S Chung

There is a common belief that the successful training of deep neural networks requires many annotated training samples, which are often expensive and difficult to obtain especially in the biomedical imaging field. While it is often easy for researchers to use data augmentation to expand the size of training sets, constructing and generating generic augmented data that is able to teach the network the desired invariance and robustness properties using traditional data augmentation techniques is challenging in practice. In this paper, we propose a novel automatic data augmentation method that uses generative adversarial networks to learn augmentations that enable machine learning based method to learn the available annotated samples more efficiently. The architecture consists of a coarse-to-fine generator to capture the manifold of the training sets and generate generic augmented data. In our experiments, we show the efficacy of our approach on a Magnetic Resonance Imaging (MRI) image, achieving improvements of 3.5% Dice coefficient on the BRATS15 Challenge dataset as compared to traditional augmentation approaches. Also, our proposed method successfully boosts a common segmentation network to reach the state-of-the-art performance on the BRATS15 Challenge.