A Deep Learning Lung Cancer Segmentation Pipeline to Facilitate CT-based Radiomics

BackgroundCT-based radio-biomarkers could provide non-invasive insights into tumour biology to risk-stratify patients. One of the limitations is laborious manual segmentation of regions-of-interest (ROI). We present a deep learning auto-segmentation pipeline for radiomic analysis. Patients and Methods153 patients with resected stage 2A-3B non-small cell lung cancer (NSCLCs) had tumours segmented using nnU-Net with review by two clinicians. The nnU-Net was pretrained with anatomical priors in non-cancerous lungs and finetuned on NSCLCs. Three ROIs were segmented: intra-tumoural, peri-tumoural, and whole lung. 1967 features were extracted using PyRadiomics. Feature reproducibility was tested using segmentation perturbations. Features were selected using minimum-redundancy-maximum-relevance with Random Forest-recursive feature elimination nested in 500 bootstraps. ResultsAuto-segmentation time was [~]36 seconds/series. Mean volumetric and surface Dice-Sorensen coefficient (DSC) scores were 0.84 ({+/-}0.28), and 0.79 ({+/-}0.34) respectively. DSC were significantly correlated with tumour shape (sphericity, diameter) and location (worse with chest wall adherence), but not batch effects (e.g. contrast, reconstruction kernel). 6.5% cases had missed segmentations; 6.5% required major changes. Pre-training on anatomical priors resulted in better segmentations compared to training on tumour-labels alone (p<0.001) and tumour with anatomical labels (p<0.001). Most radiomic features were not reproducible following perturbations and resampling. Adding radiomic features, however, did not significantly improve the clinical model in predicting 2-year disease-free survival: AUCs 0.67 (95%CI 0.59-0.75) vs 0.63 (95%CI 0.54-0.71) respectively (p=0.28). ConclusionOur study demonstrates that integrating auto-segmentation into radio-biomarker discovery is feasible with high efficiency and accuracy. Whilst radiomic analysis show limited reproducibility, our auto-segmentation may allow more robust radio-biomarker analysis using deep learning features.