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Automated identification and quantification of metastatic brain tumors and perilesional edema based on a deep learning neural network

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This paper presents a deep learning model for use in the automated segmentation of metastatic brain tumors and associated perilesional edema.


The model was trained using Gamma Knife surgical data (90 MRI sets from 46 patients), including the initial treatment plan and follow-up images (T1-weighted contrast-enhanced (T1cWI) and T2-weighted images (T2WI)) manually annotated by neurosurgeons to indicate the target tumor and edema regions. A mask region-based convolutional neural network was used to extract brain parenchyma, after which the DeepMedic 3D convolutional neural network was in the segmentation of tumors and edemas.


Five-fold cross-validation demonstrated the efficacy of the brain parenchyma extraction model, achieving a Dice similarity coefficient of 96.4%. The segmentation models used for metastatic tumors and brain edema achieved Dice similarity coefficients of 71.6% and 85.1%, respectively. This study also presents an intuitive graphical user interface to facilitate the use of these models in clinical analysis.


This paper introduces a deep learning model for the automated segmentation and quantification of brain metastatic tumors and perilesional edema trained using only T1cWI and T2WI. This technique could facilitate further research on metastatic tumors and perilesional edema as well as other intracranial lesions.

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Data availability

The datasets generated and/or analyzed during the current study are not publicly available, but they are available from the corresponding author on reasonable request. Note that all data was anonymized during the data evaluation process.


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This work was financially supported in part by the National Science and Technology Council, Taiwan, under the project NSTC 112-2628-E-038-001-MY3, and in part by the Higher Education Sprout Project by the Ministry of Education (MOE), Taiwan. We thank the National Center for High-performance Computing (NCHC) of National Applied Research Laboratories (NARLabs) in Taiwan for providing computational and storage resources.

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Conceptualization, supervision, and project administration were performed by Chi-Jen Chou and Syu-Jyun Peng. The original draft was written by Chi-Jen Chou and Syu-Jyun Peng and all authors commented on previous versions of the manuscript. Data curation, formal analysis, software and methodology selection were performed by Chi-Jen Chou, Huai-Che Yang, Po-Yao Chang, and Syu-Jyun Peng. Investigation, data sourcing, and visualization were performed by Chi-Jen Chou, Huai-Che Yang, Ching-Jen Chen, Hsiu-Mei Wu, Chun-Fu Lin, I-Chun Lai, and Syu-Jyun Peng. All authorshave read and approved the final manuscript.

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Correspondence to Syu-Jyun Peng.

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Chou, CJ., Yang, HC., Chang, PY. et al. Automated identification and quantification of metastatic brain tumors and perilesional edema based on a deep learning neural network. J Neurooncol 166, 167–174 (2024).

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