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Register a new userDilated Convolutions in Neural Networks for Left Atrial Segmentation in 3D Gadolinium Enhanced-MRI
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Sulaiman Vesal
Publication date
2018
fields
Informatics Engineering
and research's language is
English
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Segmentation of the left atrial chamber and assessing its morphology, are essential for improving our understanding of atrial fibrillation, the most common type of cardiac arrhythmia. Automation of this process in 3D gadolinium enhanced-MRI (GE-MRI) data is desirable, as manual delineation is time-consuming, challenging and observer-dependent. Recently, deep convolutional neural networks (CNNs) have gained tremendous traction and achieved state-of-the-art results in medical image segmentation. However, it is difficult to incorporate local and global information without using contracting (pooling) layers, which in turn reduces segmentation accuracy for smaller structures. In this paper, we propose a 3D CNN for volumetric segmentation of the left atrial chamber in LGE-MRI. Our network is based on the well known U-Net architecture. We employ a 3D fully convolutional network, with dilated convolutions in the lowest level of the network, and residual connections between encoder blocks to incorporate local and global knowledge. The results show that including global context through the use of dilated convolutions, helps in domain adaptation, and the overall segmentation accuracy is improved in comparison to a 3D U-Net.
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Purpose: Atrial fibrillation (AF) is the most common cardiac arrhythmia and is correlated with increased morbidity and mortality. It is associated with atrial fibrosis, which may be assessed non-invasively using late gadolinium-enhanced (LGE) magnetic resonance imaging (MRI) where scar tissue is visualised as a region of signal enhancement. In this study, we proposed a novel fully automatic pipeline to achieve an accurate and objective atrial scarring segmentation and assessment of LGE MRI scans for the AF patients. Methods: Our fully automatic pipeline uniquely combined: (1) a multi-atlas based whole heart segmentation (MA-WHS) to determine the cardiac anatomy from an MRI Roadmap acquisition which is then mapped to LGE MRI, and (2) a super-pixel and supervised learning based approach to delineate the distribution and extent of atrial scarring in LGE MRI. Results: Both our MA-WHS and atrial scarring segmentation showed accurate delineations of cardiac anatomy (mean Dice = 89%) and atrial scarring (mean Dice =79%) respectively compared to the established ground truth from manual segmentation. Compared with previously studied methods with manual interventions, our innovative pipeline demonstrated comparable results, but was computed fully automatically. Conclusion: The proposed segmentation methods allow LGE MRI to be used as an objective assessment tool for localisation, visualisation and quantification of atrial scarring.
Dilated Convolutions have been shown to be highly useful for the task of image segmentation. By introducing gaps into convolutional filters, they enable the use of larger receptive fields without increasing the original kernel size. Even though this allows for the inexpensive capturing of features at different scales, the structure of the dilated convolutional filter leads to a loss of information. We hypothesise that inexpensive modifications to Dilated Convolutional Neural Networks, such as additional averaging layers, could overcome this limitation. In this project we test this hypothesis by evaluating the effect of these modifications for a state-of-the art image segmentation system and compare them to existing approaches with the same objective. Our experiments show that our proposed methods improve the performance of dilated convolutions for image segmentation. Crucially, our modifications achieve these results at a much lower computational cost than previous smoothing approaches.
The attention mechanism provides a sequential prediction framework for learning spatial models with enhanced implicit temporal consistency. In this work, we show a systematic design (from 2D to 3D) for how conventional networks and other forms of constraints can be incorporated into the attention framework for learning long-range dependencies for the task of pose estimation. The contribution of this paper is to provide a systematic approach for designing and training of attention-based models for the end-to-end pose estimation, with the flexibility and scalability of arbitrary video sequences as input. We achieve this by adapting temporal receptive field via a multi-scale structure of dilated convolutions. Besides, the proposed architecture can be easily adapted to a causal model enabling real-time performance. Any off-the-shelf 2D pose estimation systems, e.g. Mocap libraries, can be easily integrated in an ad-hoc fashion. Our method achieves the state-of-the-art performance and outperforms existing methods by reducing the mean per joint position error to 33.4 mm on Human3.6M dataset.
Late gadolinium enhancement magnetic resonance imaging (LGE MRI) is commonly used to visualize and quantify left atrial (LA) scars. The position and extent of scars provide important information of the pathophysiology and progression of atrial fibrillation (AF). Hence, LA scar segmentation and quantification from LGE MRI can be useful in computer-assisted diagnosis and treatment stratification of AF patients. Since manual delineation can be time-consuming and subject to intra- and inter-expert variability, automating this computing is highly desired, which nevertheless is still challenging and under-researched. This paper aims to provide a systematic review on computing methods for LA cavity, wall, scar and ablation gap segmentation and quantification from LGE MRI, and the related literature for AF studies. Specifically, we first summarize AF-related imaging techniques, particularly LGE MRI. Then, we review the methodologies of the four computing tasks in detail, and summarize the validation strategies applied in each task. Finally, the possible future developments are outlined, with a brief survey on the potential clinical applications of the aforementioned methods. The review shows that the research into this topic is still in early stages. Although several methods have been proposed, especially for LA segmentation, there is still large scope for further algorithmic developments due to performance issues related to the high variability of enhancement appearance and differences in image acquisition.
Dilated convolutions are widely used in deep semantic segmentation models as they can enlarge the filters receptive field without adding additional weights nor sacrificing spatial resolution. However, as dilated convolutional filters do not possess positional knowledge about the pixels on semantically meaningful contours, they could lead to ambiguous predictions on object boundaries. In addition, although dilating the filter can expand its receptive field, the total number of sampled pixels remains unchanged, which usually comprises a small fraction of the receptive fields total area. Inspired by the Lateral Inhibition (LI) mechanisms in human visual systems, we propose the dilated convolution with lateral inhibitions (LI-Convs) to overcome these limitations. Introducing LI mechanisms improves the convolutional filters sensitivity to semantic object boundaries. Moreover, since LI-Convs also implicitly take the pixels from the laterally inhibited zones into consideration, they can also extract features at a denser scale. By integrating LI-Convs into the Deeplabv3+ architecture, we propose the Lateral Inhibited Atrous Spatial Pyramid Pooling (LI-ASPP), the Lateral Inhibited MobileNet-V2 (LI-MNV2) and the Lateral Inhibited ResNet (LI-ResNet). Experimental results on three benchmark datasets (PASCAL VOC 2012, CelebAMask-HQ and ADE20K) show that our LI-based segmentation models outperform the baseline on all of them, thus verify the effectiveness and generality of the proposed LI-Convs.
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