Large-scale multi-center CT and MRI segmentation of pancreas with deep learning
Zheyuan Zhang, Elif Keleş, Görkem Durak, Yavuz Taktak, Onkar Susladkar, Vandan Gorade, Debesh Jha, Asli C. Ormeci, Alpay Medetalibeyoğlu, Lanhong Yao, Bin Wang, Ilkin Isler, Linkai Peng, Hongyi Pan, Camila Lopes Vendrami, Amir Bourhani, Yury Velichko, Boqing Gong, Concetto Spampinato, Ayis Pyrros, Pallavi Tiwari, Derk C.F. Klatte, Megan Engels, Sanne Hoogenboom, Candice W. Bolan, Emil Agarunov, Nassier Harfouch, Chenchan Huang, Marco J. Bruno, Ivo G. Schoots, Rajesh N. Keswani, Frank H. Miller, Tamas A. Gonda, Cemal Yazıcı, Temel Tirkes, Barış Türkbey, Michael B. Wallace, Ulaş Bağcı
Abstract
Automated volumetric segmentation of the pancreas on cross-sectional imaging is needed for diagnosis and follow-up of pancreatic diseases. While CT-based pancreatic segmentation is more established, MRI-based segmentation methods are understudied, largely due to a lack of publicly available datasets, benchmarking research efforts, and domain-specific deep learning methods. In this retrospective study, we collected a large dataset (767 scans from 499 participants) of T1-weighted (T1 W) and T2-weighted (T2 W) abdominal MRI series from five centers between March 2004 and November 2022. We also collected CT scans of 1,350 patients from publicly available sources for benchmarking purposes. We introduced a new pancreas segmentation method, called PanSegNet , combining the strengths of nnUNet and a Transformer network with a new linear attention module enabling volumetric computation. We tested PanSegNet ’s accuracy in cross-modality (a total of 2,117 scans) and cross-center settings with Dice and Hausdorff distance (HD95) evaluation metrics. We used Cohen’s kappa statistics for intra and inter-rater agreement evaluation and paired t-tests for volume and Dice comparisons, respectively. For segmentation accuracy, we achieved Dice coefficients of 88.3% (±7.2%, at case level) with CT, 85.0% (±7.9%) with T1 W MRI, and 86.3% (±6.4%) with T2 W MRI. There was a high correlation for pancreas volume prediction with R 2 of 0.91, 0.84, and 0.85 for CT, T1 W, and T2 W, respectively. We found moderate inter-observer (0.624 and 0.638 for T1 W and T2 W MRI, respectively) and high intra-observer agreement scores. All MRI data is made available at https://osf.io/kysnj/ . Our source code is available at https://github.com/NUBagciLab/PaNSegNet . • We develop a first-ever cross-platform compatible (T1 W, T2 W, and CT) pancreas segmentation tool, named PanSegNet . • PaNSegNet has innovative “linear self-attention” blocks to reduce computational cost significantly while operating on 3D. • We shared our both source code and multi-center multi-contrast MRI datasets with ground truths. • PaNSegNet underwent rigorous validation, including cross-domain and multi-center comparisons between CT and MRI scans.