Automatic segmentation of MRI images for brain radiotherapy planning using deep ensemble learning

Background and Purpose: This study aimed to develop and evaluate an efficient method to automatically segment T1- and T2-weighted brain magnetic resonance imaging (MRI) images. We specifically compared the segmentation performance of individual convolutional neural network (CNN) models against an ensemble approach to advance the accuracy of MRI-guided radiotherapy (RT) planning. Materials and Methods. The evaluation was conducted on a private clinical dataset and a publicly available dataset (HaN-Seg). Anonymized MRI data from 55 brain cancer patients, including T1-weighted, T1-weighted with contrast, and T2-weighted images, were used in the clinical dataset. We employed an EDL strategy that integrated five independently trained 2D neural networks, each tailored for precise segmentation of tumors and organs at risk (OARs) in the MRI scans. Class probabilities were obtained by averaging the final layer activations (Softmax outputs) from the five networks using a weighted-average method, which were then converted into discrete labels. Segmentation performance was evaluated using the Dice similarity coefficient (DSC) and Hausdorff distance at 95% (HD95). The EDL model was also tested on the HaN-Seg public dataset for comparison. Results. The EDL model demonstrated superior segmentation performance on both the clinical and public datasets. For the clinical dataset, the ensemble approach achieved an average DSC of 0.7 +/- 0.2 and HD95 of 4.5 +/- 2.5 mm across all segmentations, significantly outperforming individual networks which yielded DSC values <= 0.6 and HD95 values >= 14 mm. Similar improvements were observed in the HaN-Seg public dataset. Conclusions. Our study shows that the EDL model consistently outperforms individual CNN networks in both clinical and public datasets, demonstrating the potential of ensemble learning to enhance segmentation accuracy. These findings underscore the value of the EDL approach for clinical applications, particularly in MRI-guided RT planning.