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Add to EdgeBayesian Intrinsic Groupwise Image Registration: Unsupervised Disentanglement of Anatomy and Geometry
Jan 04, 2024
This article presents a general Bayesian learning framework for multi-modal groupwise registration on medical images. The method builds on probabilistic modelling of the image generative process, where the underlying common anatomy and geometric variations of the observed images are explicitly disentangled as latent variables. Thus, groupwise registration is achieved through the solution to Bayesian inference. We propose a novel hierarchical variational auto-encoding architecture to realize the inference procedure of the latent variables, where the registration parameters can be calculated in a mathematically interpretable fashion. Remarkably, this new paradigm can learn groupwise registration in an unsupervised closed-loop self-reconstruction process, sparing the burden of designing complex intensity-based similarity measures. The computationally efficient disentangled architecture is also inherently scalable and flexible, allowing for groupwise registration on large-scale image groups with variable sizes. Furthermore, the inferred structural representations from disentanglement learning are capable of capturing the latent anatomy of the observations with visual semantics. Extensive experiments were conducted to validate the proposed framework, including four datasets from cardiac, brain and abdominal medical images. The results have demonstrated the superiority of our method over conventional similarity-based approaches in terms of accuracy, efficiency, scalability and interpretability.
$\mathcal{X}$-Metric: An N-Dimensional Information-Theoretic Framework for Groupwise Registration and Deep Combined Computing
Nov 03, 2022
This paper presents a generic probabilistic framework for estimating the statistical dependency and finding the anatomical correspondences among an arbitrary number of medical images. The method builds on a novel formulation of the $N$-dimensional joint intensity distribution by representing the common anatomy as latent variables and estimating the appearance model with nonparametric estimators. Through connection to maximum likelihood and the expectation-maximization algorithm, an information\hyp{}theoretic metric called $\mathcal{X}$-metric and a co-registration algorithm named $\mathcal{X}$-CoReg are induced, allowing groupwise registration of the $N$ observed images with computational complexity of $\mathcal{O}(N)$. Moreover, the method naturally extends for a weakly-supervised scenario where anatomical labels of certain images are provided. This leads to a combined\hyp{}computing framework implemented with deep learning, which performs registration and segmentation simultaneously and collaboratively in an end-to-end fashion. Extensive experiments were conducted to demonstrate the versatility and applicability of our model, including multimodal groupwise registration, motion correction for dynamic contrast enhanced magnetic resonance images, and deep combined computing for multimodal medical images. Results show the superiority of our method in various applications in terms of both accuracy and efficiency, highlighting the advantage of the proposed representation of the imaging process.
Bayesian intrinsic groupwise registration via explicit hierarchical disentanglement
Jun 06, 2022
Previous methods on multimodal groupwise registration typically require certain highly specialized similarity metrics with restrained applicability. In this work, we instead propose a general framework which formulates groupwise registration as a procedure of hierarchical Bayesian inference. Here, the imaging process of multimodal medical images, including shape transition and appearance variation, is characterized by a disentangled variational auto-encoder. To this end, we propose a novel variational posterior and network architecture that facilitate joint learning of the common structural representation and the desired spatial correspondences. The performance of the proposed model was validated on two publicly available multimodal datasets, i.e., BrainWeb and MS-CMR of the heart. Results have demonstrated the efficacy of our framework in realizing multimodal groupwise registration in an end-to-end fashion.
MyoPS: A Benchmark of Myocardial Pathology Segmentation Combining Three-Sequence Cardiac Magnetic Resonance Images
Jan 10, 2022
Assessment of myocardial viability is essential in diagnosis and treatment management of patients suffering from myocardial infarction, and classification of pathology on myocardium is the key to this assessment. This work defines a new task of medical image analysis, i.e., to perform myocardial pathology segmentation (MyoPS) combining three-sequence cardiac magnetic resonance (CMR) images, which was first proposed in the MyoPS challenge, in conjunction with MICCAI 2020. The challenge provided 45 paired and pre-aligned CMR images, allowing algorithms to combine the complementary information from the three CMR sequences for pathology segmentation. In this article, we provide details of the challenge, survey the works from fifteen participants and interpret their methods according to five aspects, i.e., preprocessing, data augmentation, learning strategy, model architecture and post-processing. In addition, we analyze the results with respect to different factors, in order to examine the key obstacles and explore potential of solutions, as well as to provide a benchmark for future research. We conclude that while promising results have been reported, the research is still in the early stage, and more in-depth exploration is needed before a successful application to the clinics. Note that MyoPS data and evaluation tool continue to be publicly available upon registration via its homepage (www.sdspeople.fudan.edu.cn/zhuangxiahai/0/myops20/).
A low-rank representation for unsupervised registration of medical images
May 20, 2021
Registration networks have shown great application potentials in medical image analysis. However, supervised training methods have a great demand for large and high-quality labeled datasets, which is time-consuming and sometimes impractical due to data sharing issues. Unsupervised image registration algorithms commonly employ intensity-based similarity measures as loss functions without any manual annotations. These methods estimate the parameterized transformations between pairs of moving and fixed images through the optimization of the network parameters during training. However, these methods become less effective when the image quality varies, e.g., some images are corrupted by substantial noise or artifacts. In this work, we propose a novel approach based on a low-rank representation, i.e., Regnet-LRR, to tackle the problem. We project noisy images into a noise-free low-rank space, and then compute the similarity between the images. Based on the low-rank similarity measure, we train the registration network to predict the dense deformation fields of noisy image pairs. We highlight that the low-rank projection is reformulated in a way that the registration network can successfully update gradients. With two tasks, i.e., cardiac and abdominal intra-modality registration, we demonstrate that the low-rank representation can boost the generalization ability and robustness of models as well as bring significant improvements in noisy data registration scenarios.
Anatomy Prior Based U-net for Pathology Segmentation with Attention
Nov 17, 2020
Pathological area segmentation in cardiac magnetic resonance (MR) images plays a vital role in the clinical diagnosis of cardiovascular diseases. Because of the irregular shape and small area, pathological segmentation has always been a challenging task. We propose an anatomy prior based framework, which combines the U-net segmentation network with the attention technique. Leveraging the fact that the pathology is inclusive, we propose a neighborhood penalty strategy to gauge the inclusion relationship between the myocardium and the myocardial infarction and no-reflow areas. This neighborhood penalty strategy can be applied to any two labels with inclusive relationships (such as the whole infarction and myocardium, etc.) to form a neighboring loss. The proposed framework is evaluated on the EMIDEC dataset. Results show that our framework is effective in pathological area segmentation.
MvMM-RegNet: A new image registration framework based on multivariate mixture model and neural network estimation
Jul 14, 2020
Current deep-learning-based registration algorithms often exploit intensity-based similarity measures as the loss function, where dense correspondence between a pair of moving and fixed images is optimized through backpropagation during training. However, intensity-based metrics can be misleading when the assumption of intensity class correspondence is violated, especially in cross-modality or contrast-enhanced images. Moreover, existing learning-based registration methods are predominantly applicable to pairwise registration and are rarely extended to groupwise registration or simultaneous registration with multiple images. In this paper, we propose a new image registration framework based on multivariate mixture model (MvMM) and neural network estimation. A generative model consolidating both appearance and anatomical information is established to derive a novel loss function capable of implementing groupwise registration. We highlight the versatility of the proposed framework for various applications on multimodal cardiac images, including single-atlas-based segmentation (SAS) via pairwise registration and multi-atlas segmentation (MAS) unified by groupwise registration. We evaluated performance on two publicly available datasets, i.e. MM-WHS-2017 and MS-CMRSeg-2019. The results show that the proposed framework achieved an average Dice score of $0.871\pm 0.025$ for whole-heart segmentation on MR images and $0.783\pm 0.082$ for myocardium segmentation on LGE MR images.
Cardiac Segmentation on Late Gadolinium Enhancement MRI: A Benchmark Study from Multi-Sequence Cardiac MR Segmentation Challenge
Jun 22, 2020
Accurate computing, analysis and modeling of the ventricles and myocardium from medical images are important, especially in the diagnosis and treatment management for patients suffering from myocardial infarction (MI). Late gadolinium enhancement (LGE) cardiac magnetic resonance (CMR) provides an important protocol to visualize MI. However, automated segmentation of LGE CMR is still challenging, due to the indistinguishable boundaries, heterogeneous intensity distribution and complex enhancement patterns of pathological myocardium from LGE CMR. Furthermore, compared with the other sequences LGE CMR images with gold standard labels are particularly limited, which represents another obstacle for developing novel algorithms for automatic segmentation of LGE CMR. This paper presents the selective results from the Multi-Sequence Cardiac MR (MS-CMR) Segmentation challenge, in conjunction with MICCAI 2019. The challenge offered a data set of paired MS-CMR images, including auxiliary CMR sequences as well as LGE CMR, from 45 patients who underwent cardiomyopathy. It was aimed to develop new algorithms, as well as benchmark existing ones for LGE CMR segmentation and compare them objectively. In addition, the paired MS-CMR images could enable algorithms to combine the complementary information from the other sequences for the segmentation of LGE CMR. Nine representative works were selected for evaluation and comparisons, among which three methods are unsupervised methods and the other six are supervised. The results showed that the average performance of the nine methods was comparable to the inter-observer variations. The success of these methods was mainly attributed to the inclusion of the auxiliary sequences from the MS-CMR images, which provide important label information for the training of deep neural networks.
A Global Benchmark of Algorithms for Segmenting Late Gadolinium-Enhanced Cardiac Magnetic Resonance Imaging
May 07, 2020
Segmentation of cardiac images, particularly late gadolinium-enhanced magnetic resonance imaging (LGE-MRI) widely used for visualizing diseased cardiac structures, is a crucial first step for clinical diagnosis and treatment. However, direct segmentation of LGE-MRIs is challenging due to its attenuated contrast. Since most clinical studies have relied on manual and labor-intensive approaches, automatic methods are of high interest, particularly optimized machine learning approaches. To address this, we organized the "2018 Left Atrium Segmentation Challenge" using 154 3D LGE-MRIs, currently the world's largest cardiac LGE-MRI dataset, and associated labels of the left atrium segmented by three medical experts, ultimately attracting the participation of 27 international teams. In this paper, extensive analysis of the submitted algorithms using technical and biological metrics was performed by undergoing subgroup analysis and conducting hyper-parameter analysis, offering an overall picture of the major design choices of convolutional neural networks (CNNs) and practical considerations for achieving state-of-the-art left atrium segmentation. Results show the top method achieved a dice score of 93.2% and a mean surface to a surface distance of 0.7 mm, significantly outperforming prior state-of-the-art. Particularly, our analysis demonstrated that double, sequentially used CNNs, in which a first CNN is used for automatic region-of-interest localization and a subsequent CNN is used for refined regional segmentation, achieved far superior results than traditional methods and pipelines containing single CNNs. This large-scale benchmarking study makes a significant step towards much-improved segmentation methods for cardiac LGE-MRIs, and will serve as an important benchmark for evaluating and comparing the future works in the field.
Cardiac Segmentation from LGE MRI Using Deep Neural Network Incorporating Shape and Spatial Priors
Jun 25, 2019
Cardiac segmentation from late gadolinium enhancement MRI is an important task in clinics to identify and evaluate the infarction of myocardium. The automatic segmentation is however still challenging, due to the heterogeneous intensity distributions and indistinct boundaries in the images. In this paper, we propose a new method, based on deep neural networks (DNN), for fully automatic segmentation. The proposed network, referred to as SRSCN, comprises a shape reconstruction neural network (SRNN) and a spatial constraint network (SCN). SRNN aims to maintain a realistic shape of the resulting segmentation. It can be pre-trained by a set of label images, and then be embedded into a unified loss function as a regularization term. Hence, no manually designed feature is needed. Furthermore, SCN incorporates the spatial information of the 2D slices. It is formulated and trained with the segmentation network via the multi-task learning strategy. We evaluated the proposed method using 45 patients and compared with two state-of-the-art regularization schemes, i.e., the anatomically constraint neural network and the adversarial neural network. The results show that the proposed SRSCN outperformed the conventional schemes, and obtained a Dice score of 0.758(std=0.227) for myocardial segmentation, which compares with 0.757(std=0.083) from the inter-observer variations.