AutoPET III Challenge: Tumor Lesion Segmentation using ResEnc-Model Ensemble

TL;DR

This paper presents a deep learning approach using a 3D Residual encoder U-Net with ensemble techniques for tumor lesion segmentation in PET/CT scans, achieving top performance in the AutoPET III challenge.

Contribution

The study introduces a robust segmentation model that generalizes across multiple tracers and centers, utilizing advanced preprocessing, test-time augmentation, and ensemble methods.

Findings

Achieved a Dice score of 0.9627 on the challenge test set.

Outperformed baseline models in the AutoPET III challenge.

Demonstrated effective generalization across different tracers and clinical sites.

Abstract

Positron Emission Tomography (PET) /Computed Tomography (CT) is crucial for diagnosing, managing, and planning treatment for various cancers. Developing reliable deep learning models for the segmentation of tumor lesions in PET/CT scans in a multi-tracer multicenter environment, is a critical area of research. Different tracers, such as Fluorodeoxyglucose (FDG) and Prostate-Specific Membrane Antigen (PSMA), have distinct physiological uptake patterns and data from different centers often vary in terms of acquisition protocols, scanner types, and patient populations. Because of this variability, it becomes more difficult to design reliable segmentation algorithms and generalization techniques due to variations in image quality and lesion detectability. To address this challenge, We trained a 3D Residual encoder U-Net within the no new U-Net framework, aiming to generalize the performance of automatic lesion segmentation of whole body PET/CT scans, across different tracers and clinical sites. Further, We explored several preprocessing techniques and ultimately settled on using the Total Segmentator to crop our training data. Additionally, we applied resampling during this process. During inference, we leveraged test-time augmentations and other post-processing techniques to enhance tumor lesion segmentation. Our team currently hold the top position in the Auto-PET III challenge and outperformed the challenge baseline model in the preliminary test set with Dice score of 0.9627.