An improved attention module based on nnU-Net for segmenting primary central nervous system lymphoma (PCNSL) in MRI images¹

Article type: Research Article

Authors: Zhao, Chen^a | Song, Jianping^{b; c} | Yuan, Yifan^{b; c; *} | Chu, Ying-Hua^d | Hsu, Yi-Cheng^d | Huang, Qiu^{e; *}

Affiliations: [a] School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China | [b] Department of Neurosurgery, National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai, China | [c] Department of Neurosurgery, National Regional Medical Center, Huashan Hospital Fujian Campus, Fudan University, Fuzhou, Fujian, China | [d] Siemens Healthineers Ltd., Shanghai, China | [e] Department of Nuclear Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China

Correspondence: [*] Corresponding authors:Yifan Yuan, Department of Neurosurgery, National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai 200040, China. E-mail: yuanyifanhs@126.com and Qiu Huang, Member, IEEE, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China, and also with the Department of Nuclear Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China. E-mail: qiuhuang@sjtu.edu.cn.

Note: [1] Thisworkwas supported by Fujian Province Science and Technology Innovation Joint Fund under Grant No. 2021Y9135, Pudong NewArea Science and Technology Development Fund under Grant No. PKX2020-R03, Shanghai Municipal Alliance for Clinical Competence Improvement and Advancement in Neurosurgery under Grant SHDC22021303.

Abstract: BACKGROUND: Accurate volumetric segmentation of primary central nervous system lymphoma (PCNSL) is essential for assessing and monitoring the tumor before radiotherapy and the treatment planning. The tedious manual segmentation leads to interindividual and intraindividual differences, while existing automatic segmentation methods cause under-segmentation of PCNSL due to the complex and multifaceted nature of the tumor. OBJECTIVE: To address the challenges of small size, diffused distribution, poor inter-layer continuity on the same axis, and tendency for over-segmentation in brain MRI PCNSL segmentation, we propose an improved attention module based on nnUNet for automated segmentation. METHODS: We collected 114 T1 MRI images of patients in the Huashan Hospital, Shanghai. Then randomly split the total of 114 cases into 5 distinct training and test sets for a 5-fold cross-validation. To efficiently and accurately delineate the PCNSL, we proposed an improved attention module based on nnU-Net with 3D convolutions, batch normalization, and residual attention (res-attention) to learn the tumor region information. Additionally, multi-scale dilated convolution kernels with different dilation rates were integrated to broaden the receptive field. We further used attentional feature fusion with 3D convolutions (AFF3D) to fuse the feature maps generated by multi-scale dilated convolution kernels to reduce under-segmentation. RESULTS: Compared to existing methods, our attention module improves the ability to distinguish diffuse and edge enhanced types of tumors; and the broadened receptive field captures tumor features of various scales and shapes more effectively, achieving a 0.9349 Dice Similarity Coefficient (DSC). CONCLUSIONS: Quantitative results demonstrate the effectiveness of the proposed method in segmenting the PCNSL. To our knowledge, this is the first study to introduce attention modules into deep learning for segmenting PCNSL based on brain magnetic resonance imaging (MRI), promoting the localization of PCNSL before radiotherapy.

Keywords: Primary central nervous system lymphoma (PCNSL), convolutional neural network (CNN), attention, magnetic resonance imaging (MRI), segmentation

DOI: 10.3233/XST-240016

Journal: Journal of X-Ray Science and Technology, vol. 32, no. 4, pp. 993-1009, 2024