Segmentation of Pediatric Brain Tumors using a Radiologically informed, Deep Learning Cascade

Abstract: Monitoring of Diffuse Intrinsic Pontine Glioma (DIPG) and Diffuse Midline Glioma (DMG) brain tumors in pediatric patients is key for assessment of treatment response. Response Assessment in Pediatric Neuro-Oncology (RAPNO) guidelines recommend the volumetric measurement of these tumors using MRI. Segmentation challenges, such as the Brain Tumor Segmentation (BraTS) Challenge, promote development of automated approaches which are replicable, generalizable and accurate, to aid in these tasks. The current study presents a novel adaptation of existing nnU-Net approaches for pediatric brain tumor segmentation, submitted to the BraTS-PEDs 2024 challenge. We apply an adapted nnU-Net with hierarchical cascades to the segmentation task of the BraTS-PEDs 2024 challenge. The residual encoder variant of nnU-Net, used as our baseline model, already provides high quality segmentations. We incorporate multiple changes to the implementation of nnU-Net and devise a novel two-stage cascaded nnU-Net to segment the substructures of brain tumors from coarse to fine. Using outputs from the nnU-Net Residual Encoder (trained to segment CC, ED, ET and NET tumor labels from T1w, T1w-CE, T2w and T2-FLAIR MRI), these are passed to two additional models one classifying ET versus NET and a second classifying CC vs ED using cascade learning. We use radiological guidelines to steer which multi parametric MRI (mpMRI) to use in these cascading models. Compared to a default nnU-Net and an ensembled nnU-net as baseline approaches, our novel method provides robust segmentations for the BraTS-PEDs 2024 challenge, achieving mean Dice scores of 0.657, 0.904, 0.703, and 0.967, and HD95 of 76.2, 10.1, 111.0, and 12.3 for the ET, NET, CC and ED, respectively.