Convolutional neural networks (CNNs) have recently achieved remarkable success in automatically identifying organs or lesions on 3D medical images. Meanwhile, vision transformer networks have exhibited exceptional performance in 2D image classification tasks. Compared with CNNs, transformer networks have an obvious advantage of extracting long-range features due to their self-attention algorithm. Therefore, in this paper we present a CNN-Transformer combined model called BiTr-Unet for brain tumor segmentation on multi-modal MRI scans. The proposed BiTr-Unet achieves good performance on the BraTS 2021 validation dataset with mean Dice score 0.9076, 0.8392 and 0.8231, and mean Hausdorff distance 4.5322, 13.4592 and 14.9963 for the whole tumor, tumor core, and enhancing tumor, respectively.

Transformer, which can benefit from global (long-range) information modeling using self-attention mechanisms, has been successful in natural language processing and 2D image classification recently. However, both local and global features are crucial for dense prediction tasks, especially for 3D medical image segmentation. In this paper, we for the first time exploit Transformer in 3D CNN for MRI Brain Tumor Segmentation and propose a novel network named TransBTS based on the encoder-decoder structure. To capture the local 3D context information, the encoder first utilizes 3D CNN to extract the volumetric spatial feature maps. Meanwhile, the feature maps are reformed elaborately for tokens that are fed into Transformer for global feature modeling. The decoder leverages the features embedded by Transformer and performs progressive upsampling to predict the detailed segmentation map. Experimental results on the BraTS 2019 dataset show that TransBTS outperforms state-of-the-art methods for brain tumor segmentation on 3D MRI scans. Code is available at https://github.com/Wenxuan-1119/