A Global Benchmark of Algorithms for Segmenting Late Gadolinium-Enhanced Cardiac Magnetic Resonance Imaging

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.

Mutual information neural estimation in CNN-based end-to-end medical image registration

Image registration is one of the most underlined processes in medical image analysis. Recently, convolutional neural networks (CNNs) have shown significant potential in both affine and deformable registration. However, the lack of voxel-wise ground truth challenges the training of an accurate CNN-based registration. In this work, we implement a CNN-based mutual information neural estimator for image registration that evaluates the registration outputs in an unsupervised manner. Based on the estimator, we propose an end-to-end registration framework, denoted as MIRegNet, to realize one-shot affine and deformable registration. Furthermore, we propose a weakly supervised network combining mutual information with the Dice similarity coefficients (DSC) loss. We employed a dataset consisting of 190 pairs of 3D pulmonary CT images for validation. Results showed that the MIRegNet obtained an average Dice score of 0.960 for registering the pulmonary images, and the Dice score was further improved to 0.963 when the DSC was included for a weakly supervised learning of image registration.

Cardiac Segmentation from LGE MRI Using Deep Neural Network Incorporating Shape and Spatial Priors

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.

Multi-scale deep neural networks for real image super-resolution

Single image super-resolution (SR) is extremely difficult if the upscaling factors of image pairs are unknown and different from each other, which is common in real image SR. To tackle the difficulty, we develop two multi-scale deep neural networks (MsDNN) in this work. Firstly, due to the high computation complexity in high-resolution spaces, we process an input image mainly in two different downscaling spaces, which could greatly lower the usage of GPU memory. Then, to reconstruct the details of an image, we design a multi-scale residual network (MsRN) in the downscaling spaces based on the residual blocks. Besides, we propose a multi-scale dense network based on the dense blocks to compare with MsRN. Finally, our empirical experiments show the robustness of MsDNN for image SR when the upscaling factor is unknown. According to the preliminary results of NTIRE 2019 image SR challenge, our team (ZXHresearch@fudan) ranks 21-st among all participants. The implementation of MsDNN is released https://github.com/shangqigao/gsq-image-SR

A Fully-Automatic Framework for Parkinson's Disease Diagnosis by Multi-Modality Images

Background: Parkinson's disease (PD) is a prevalent long-term neurodegenerative disease. Though the diagnostic criteria of PD are relatively well defined, the current medical imaging diagnostic procedures are expertise-demanding, and thus call for a higher-integrated AI-based diagnostic algorithm. Methods: In this paper, we proposed an automatic, end-to-end, multi-modality diagnosis framework, including segmentation, registration, feature generation and machine learning, to process the information of the striatum for the diagnosis of PD. Multiple modalities, including T1- weighted MRI and 11C-CFT PET, were used in the proposed framework. The reliability of this framework was then validated on a dataset from the PET center of Huashan Hospital, as the dataset contains paired T1-MRI and CFT-PET images of 18 Normal (NL) subjects and 49 PD subjects. Results: We obtained an accuracy of 100% for the PD/NL classification task, besides, we conducted several comparative experiments to validate the diagnosis ability of our framework. Conclusion: Through experiment we illustrate that (1) automatic segmentation has the same classification effect as the manual segmentation, (2) the multi-modality images generates a better prediction than single modality images, and (3) volume feature is shown to be irrelevant to PD diagnosis.

Diagnosis of Alzheimer's Disease via Multi-modality 3D Convolutional Neural Network

Alzheimer's Disease (AD) is one of the most concerned neurodegenerative diseases. In the last decade, studies on AD diagnosis attached great significance to artificial intelligence (AI)-based diagnostic algorithms. Among the diverse modality imaging data, T1-weighted MRI and 18F-FDGPET are widely researched for this task. In this paper, we propose a novel convolutional neural network (CNN) to fuse the multi-modality information including T1-MRI and FDG-PDT images around the hippocampal area for the diagnosis of AD. Different from the traditional machine learning algorithms, this method does not require manually extracted features, and utilizes the stateof-art 3D image-processing CNNs to learn features for the diagnosis and prognosis of AD. To validate the performance of the proposed network, we trained the classifier with paired T1-MRI and FDG-PET images using the ADNI datasets, including 731 Normal (NL) subjects, 647 AD subjects, 441 stable MCI (sMCI) subjects and 326 progressive MCI (pMCI) subjects. We obtained the maximal accuracies of 90.10% for NL/AD task, 87.46% for NL/pMCI task, and 76.90% for sMCI/pMCI task. The proposed framework yields comparative results against state-of-the-art approaches. Moreover, the experimental results have demonstrated that (1) segmentation is not a prerequisite by using CNN, (2) the hippocampal area provides enough information to give a reference to AD diagnosis. Keywords: Alzheimer's Disease, Multi-modality, Image Classification, CNN, Deep Learning, Hippocampal

Evaluation of Algorithms for Multi-Modality Whole Heart Segmentation: An Open-Access Grand Challenge

Knowledge of whole heart anatomy is a prerequisite for many clinical applications. Whole heart segmentation (WHS), which delineates substructures of the heart, can be very valuable for modeling and analysis of the anatomy and functions of the heart. However, automating this segmentation can be arduous due to the large variation of the heart shape, and different image qualities of the clinical data. To achieve this goal, a set of training data is generally needed for constructing priors or for training. In addition, it is difficult to perform comparisons between different methods, largely due to differences in the datasets and evaluation metrics used. This manuscript presents the methodologies and evaluation results for the WHS algorithms selected from the submissions to the Multi-Modality Whole Heart Segmentation (MM-WHS) challenge, in conjunction with MICCAI 2017. The challenge provides 120 three-dimensional cardiac images covering the whole heart, including 60 CT and 60 MRI volumes, all acquired in clinical environments with manual delineation. Ten algorithms for CT data and eleven algorithms for MRI data, submitted from twelve groups, have been evaluated. The results show that many of the deep learning (DL) based methods achieved high accuracy, even though the number of training datasets was limited. A number of them also reported poor results in the blinded evaluation, probably due to overfitting in their training. The conventional algorithms, mainly based on multi-atlas segmentation, demonstrated robust and stable performance, even though the accuracy is not as good as the best DL method in CT segmentation. The challenge, including the provision of the annotated training data and the blinded evaluation for submitted algorithms on the test data, continues as an ongoing benchmarking resource via its homepage (\url{www.sdspeople.fudan.edu.cn/zhuangxiahai/0/mmwhs/}).

Atrial Scar Quantification via Multi-scale CNN in the Graph-cuts Framework

Late gadolinium enhancement magnetic resonance imaging (LGE MRI) appears to be a promising alternative for scar assessment in patients with atrial fibrillation (AF). Automating the quantification and analysis of atrial scars can be challenging due to the low image quality. In this work, we propose a fully automated method based on the graph-cuts framework, where the potentials of the graph are learned on a surface mesh of the left atrium (LA) using a multi-scale convolutional neural network (MS-CNN). For validation, we have employed fifty-eight images with manual delineations. MS-CNN, which can efficiently incorporate both the local and global texture information of the images, has been shown to evidently improve the segmentation accuracy of the proposed graph-cuts based method. The segmentation could be further improved when the contribution between the t-link and n-link weights of the graph is balanced. The proposed method achieves a mean accuracy of 0.856 +- 0.033 and mean Dice score of 0.702 +- 0.071 for LA scar quantification. Compared with the conventional methods, which are based on the manual delineation of LA for initialization, our method is fully automatic and has demonstrated significantly better Dice score and accuracy (p < 0.01). The method is promising and can be useful in diagnosis and prognosis of AF.

PnP-AdaNet: Plug-and-Play Adversarial Domain Adaptation Network with a Benchmark at Cross-modality Cardiac Segmentation

Deep convolutional networks have demonstrated the state-of-the-art performance on various medical image computing tasks. Leveraging images from different modalities for the same analysis task holds clinical benefits. However, the generalization capability of deep models on test data with different distributions remain as a major challenge. In this paper, we propose the PnPAdaNet (plug-and-play adversarial domain adaptation network) for adapting segmentation networks between different modalities of medical images, e.g., MRI and CT. We propose to tackle the significant domain shift by aligning the feature spaces of source and target domains in an unsupervised manner. Specifically, a domain adaptation module flexibly replaces the early encoder layers of the source network, and the higher layers are shared between domains. With adversarial learning, we build two discriminators whose inputs are respectively multi-level features and predicted segmentation masks. We have validated our domain adaptation method on cardiac structure segmentation in unpaired MRI and CT. The experimental results with comprehensive ablation studies demonstrate the excellent efficacy of our proposed PnP-AdaNet. Moreover, we introduce a novel benchmark on the cardiac dataset for the task of unsupervised cross-modality domain adaptation. We will make our code and database publicly available, aiming to promote future studies on this challenging yet important research topic in medical imaging.