A robust auto-contouring and data augmentation pipeline for adaptive MRI-guided radiotherapy of pancreatic cancer with a limited dataset.

Objective.This study aims to develop and evaluate a fast and robust deep learning-based auto-segmentation approach for organs at risk in MRI-guided radiotherapy of pancreatic cancer to overcome the problems of time-intensive manual contouring in online adaptive workflows. The research focuses on implementing novel data augmentation techniques to address the challenges posed by limited datasets.Approach.This study was conducted in two phases. In phase I, we selected and customized the best-performing segmentation model among ResU-Net, SegResNet, and nnU-Net, using 43 balanced 3DVane images from 10 patients with 5-fold cross-validation. Phase II focused on optimizing the chosen model through two advanced data augmentation approaches to improve performance and generalizability by increasing the effective input dataset: (1) a novel structure-guided deformation-based augmentation approach (sgDefAug) and (2) a generative adversarial network-based method using a cycleGAN (GANAug). These were compared with comprehensive conventional augmentations (ConvAug). The approaches were evaluated using geometric (Dice score, average surface distance (ASD)) and dosimetric (D2% and D50% from dose-volume histograms) criteria.Main results.The nnU-Net framework demonstrated superior performance (mean Dice: 0.78 ± 0.10, mean ASD: 3.92 ± 1.94 mm) compared to other models. The sgDefAug and GANAug approaches significantly improved model performance over ConvAug, with sgDefAug demonstrating slightly superior results (mean Dice: 0.84 ± 0.09, mean ASD: 3.14 ± 1.79 mm). The proposed methodology produced auto-contours in under 30 s, with 75% of organs showing less than 1% difference in D2% and D50% dose criteria compared to ground truth.Significance.The integration of the nnU-Net framework with our proposed novel augmentation technique effectively addresses the challenges of limited datasets and stringent time constraints in online adaptive radiotherapy for pancreatic cancer. Our approach offers a promising solution for streamlining online adaptive workflows and represents a substantial step forward in the practical application of auto-segmentation techniques in clinical radiotherapy settings.