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基于多模态 MRI 数据的 CNN 肿瘤分割方法的综合基准测试。

Comprehensive benchmarking of CNN-based tumor segmentation methods using multimodal MRI data.

机构信息

Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, 502284, India.

Department of Neurosurgical Oncology, Basavatarakam Indo American Cancer Hospital & Research Institute, Hyderabad, Telangana, 500034, India.

出版信息

Comput Biol Med. 2024 Aug;178:108799. doi: 10.1016/j.compbiomed.2024.108799. Epub 2024 Jun 25.


DOI:10.1016/j.compbiomed.2024.108799
PMID:38925087
Abstract

Magnetic resonance imaging (MRI) has become an essential and a frontline technique in the detection of brain tumor. However, segmenting tumors manually from scans is laborious and time-consuming. This has led to an increasing trend towards fully automated methods for precise tumor segmentation in MRI scans. Accurate tumor segmentation is crucial for improved diagnosis, treatment, and prognosis. This study benchmarks and evaluates four widely used CNN-based methods for brain tumor segmentation CaPTk, 2DVNet, EnsembleUNets, and ResNet50. Using 1251 multimodal MRI scans from the BraTS2021 dataset, we compared the performance of these methods against a reference dataset of segmented images assisted by radiologists. This comparison was conducted using segmented images directly and further by radiomic features extracted from the segmented images using pyRadiomics. Performance was assessed using the Dice Similarity Coefficient (DSC) and Hausdorff Distance (HD). EnsembleUNets excelled, achieving a DSC of 0.93 and an HD of 18, outperforming the other methods. Further comparative analysis of radiomic features confirmed EnsembleUNets as the most precise segmentation method, surpassing other methods. EnsembleUNets recorded a Concordance Correlation Coefficient (CCC) of 0.79, a Total Deviation Index (TDI) of 1.14, and a Root Mean Square Error (RMSE) of 0.53, underscoring its superior performance. We also performed validation on an independent dataset of 611 samples (UPENN-GBM), which further supported the accuracy of EnsembleUNets, with a DSC of 0.85 and an HD of 17.5. These findings provide valuable insight into the efficacy of EnsembleUNets, supporting informed decisions for accurate brain tumor segmentation.

摘要

磁共振成像(MRI)已成为检测脑肿瘤的重要且前沿的技术。然而,手动从扫描中分割肿瘤既费力又耗时。这导致了越来越多的趋势,即使用完全自动化的方法对 MRI 扫描中的精确肿瘤进行分割。准确的肿瘤分割对于改善诊断、治疗和预后至关重要。本研究基准测试和评估了四种广泛使用的基于 CNN 的脑肿瘤分割方法 CaPTk、2DVNet、EnsembleUNets 和 ResNet50。使用来自 BraTS2021 数据集的 1251 例多模态 MRI 扫描,我们将这些方法的性能与由放射科医生辅助分割的参考数据集进行了比较。这种比较是直接使用分割图像进行的,并且还使用来自分割图像的放射组学特征(使用 pyRadiomics 提取)进行了比较。使用 Dice 相似系数(DSC)和 Hausdorff 距离(HD)评估性能。EnsembleUNets 表现出色,DSC 为 0.93,HD 为 18,优于其他方法。进一步对放射组学特征的比较分析证实,EnsembleUNets 是最精确的分割方法,优于其他方法。EnsembleUNets 记录了 0.79 的一致性相关系数(CCC)、1.14 的总偏差指数(TDI)和 0.53 的均方根误差(RMSE),突出了其卓越的性能。我们还在另一个独立的 611 样本数据集(UPENN-GBM)上进行了验证,进一步支持了 EnsembleUNets 的准确性,DSC 为 0.85,HD 为 17.5。这些发现为 EnsembleUNets 的疗效提供了有价值的见解,支持了准确的脑肿瘤分割的明智决策。

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