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arXiv 1802.02427eess.IVcs.CV
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基于密集连接三维CNN的MRI肿瘤分割

MRI Tumor Segmentation with Densely Connected 3D CNN

Department of Computer Science, University of Rochester(罗切斯特大学计算机科学系);Department of Electrical Engineering, University of Rochester(罗切斯特大学电气工程系);Department of Biomedical Engineering, University of Rochester(罗切斯特大学生物医学工程系);Department of Imaging Sciences, University of Rochester(罗切斯特大学影像科学系);Faculty of Medicine and Institute of Clinical Radiology, Ludwig Maximilian University(路德维希-马克西米利安大学医学院及临床放射学研究所)

Lele Chen, Yue Wu, Adora M. DSouza, Anas Z. Abidin, Axel Wismuller, Chenliang Xu

摘要:

胶质瘤是最常见和最具侵袭性的原发性脑肿瘤之一。皮质下脑结构的准确分割对于胶质瘤的研究至关重要,因为它有助于监测胶质瘤的进展并有助于评估治疗结果。然而,所需的大量人力使得难以获得手动分割的磁共振成像(MRI)数据,从而限制了在临床实践中使用精确的定量测量。在这项工作中,我们试图解决这个问题,通过开发一个三维卷积神经网络~(3D CNN)为基础的模型来自动分割胶质瘤。我们的分割模型的主要困难来自于这样一个事实,即胶质瘤的位置,结构和形状在不同的患者之间存在显着差异。为了准确地对每个体素进行分类,我们的模型通过从两个尺度的感受野中提取特征来捕获多尺度上下文信息。为了充分利用肿瘤结构,我们提出了一种新的架构,分层分割坏死和非增强肿瘤~(NCR/NET),瘤周水肿~(ED)和GD增强肿瘤~(ET)的不同病变区域。此外,我们利用密集连接的卷积块来进一步提高性能。我们用补丁式训练模式训练我们的模型,以减轻类不平衡问题。该方法在BraTS 2017数据集上进行了验证,完整肿瘤、肿瘤核心和增强肿瘤的Dice评分分别为0.72、0.83和0.81。这些结果与报道的最先进的结果相当,并且我们的方法在紧凑性,时间和空间效率方面优于现有的基于3D的方法。

英文摘要:

Glioma is one of the most common and aggressive types of primary brain tumors. The accurate segmentation of subcortical brain structures is crucial to the study of gliomas in that it helps the monitoring of the progression of gliomas and aids the evaluation of treatment outcomes. However, the large amount of required human labor makes it difficult to obtain the manually segmented Magnetic Resonance Imaging (MRI) data, limiting the use of precise quantitative measurements in the clinical practice. In this work, we try to address this problem by developing a 3D Convolutional Neural Network~(3D CNN) based model to automatically segment gliomas. The major difficulty of our segmentation model comes with the fact that the location, structure, and shape of gliomas vary significantly among different patients. In order to accurately classify each voxel, our model captures multi-scale contextual information by extracting features from two scales of receptive fields. To fully exploit the tumor structure, we propose a novel architecture that hierarchically segments different lesion regions of the necrotic and non-enhancing tumor~(NCR/NET), peritumoral edema~(ED) and GD-enhancing tumor~(ET). Additionally, we utilize densely connected convolutional blocks to further boost the performance. We train our model with a patch-wise training schema to mitigate the class imbalance problem. The proposed method is validated on the BraTS 2017 dataset and it achieves Dice scores of 0.72, 0.83 and 0.81 for the complete tumor, tumor core and enhancing tumor, respectively. These results are comparable to the reported state-of-the-art results, and our method is better than existing 3D-based methods in terms of compactness, time and space efficiency.

机构、总结、中文摘要均由AI分析而来,可能存在错误,请以论文正文为准。

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