On-the-Fly Data Augmentation for Brain Tumor Segmentation

Abstract: Robust segmentation across both pre-treatment and post-treatment glioma scans can be helpful for consistent tumor monitoring and treatment planning. BraTS 2025 Task 1 addresses this by challenging models to generalize across varying tumor appearances throughout the treatment timeline. However, training such generalized models requires access to diverse, high-quality annotated data, which is often limited. While data augmentation can alleviate this, storing large volumes of augmented 3D data is computationally expensive. To address these challenges, we propose an on-the-fly augmentation strategy that dynamically inserts synthetic tumors using pretrained generative adversarial networks (GliGANs) during training. We evaluate three nnU-Net-based models and their ensembles: (1) a baseline without external augmentation, (2) a regular on-the-fly augmented model, and (3) a model with customized on-the-fly augmentation. Built upon the nnU-Net framework, our pipeline leverages pretrained GliGAN weights and tumor insertion methods from prior challenge-winning solutions. An ensemble of the three models achieves lesion-wise Dice scores of 0.79 (ET), 0.749 (NETC), 0.872 (RC), 0.825 (SNFH), 0.79 (TC), and 0.88 (WT) on the online BraTS 2025 validation platform. This work ranked first in the BraTS Lighthouse Challenge 2025 Task 1- Adult Glioma Segmentation.