Joint Brain Tumor Segmentation from Multi-magnetic Resonance Sequences through a Deep Convolutional Neural Network

Abstract Background: Brain tumor segmentation is highly contributive in diagnosing and treatment planning. Manual brain tumor delineation is a time-consuming and tedious task and varies depending on the radiologist’s skill. Automated brain tumor segmentation is of high importance and does not depend on either inter- or intra-observation. The objective of this study is to automate the delineation of brain tumors from the Fluid-attenuated inversion recovery (FLAIR), T1-weighted (T1W), T2-weighted (T2W), and T1W contrast-enhanced (T1ce) magnetic resonance (MR) sequences through a deep learning approach, with a focus on determining which MR sequence alone or which combination thereof would lead to the highest accuracy therein. Methods: The BraTS-2020 challenge dataset, containing 370 subjects with four MR sequences and manually delineated tumor masks, is applied to train a residual neural network. This network is trained and assessed separately for each one of the MR sequences (single-channel input) and any combination thereof (dual- or multi-channel input). Results: The quantitative assessment of the single-channel models reveals that the FLAIR sequence would yield higher segmentation accuracy compared to its counterparts with a 0.77 ± 0.10 Dice index. As to considering the dual-channel models, the model with FLAIR and T2W inputs yields a 0.80 ± 0.10 Dice index, exhibiting higher performance. The joint tumor segmentation on the entire four MR sequences yields the highest overall segmentation accuracy with a 0.82 ± 0.09 Dice index. Conclusion: The FLAIR MR sequence is considered the best choice for tumor segmentation on a single MR sequence, while the joint segmentation on the entire four MR sequences would yield higher tumor delineation accuracy.