MRI lung lobe segmentation in pediatric cystic fibrosis patients using a recurrent neural network trained with publicly accessible CT datasets. Issue 1 (29th March 2022)

• Record Type: Journal Article
• Authors: Pusterla, Orso; Heule, Rahel; Santini, Francesco; Weikert, Thomas; Willers, Corin; Andermatt, Simon; Sandkühler, Robin; Nyilas, Sylvia; Latzin, Philipp; Bieri, Oliver; Bauman, Grzegorz
• Is Part Of: Magnetic resonance in medicine. Volume 88:Issue 1(2022)
• Page Start: 391
• Page End: 405
• Publication Date: 2022-03-29
• Subjects: automated segmentation -- computed tomography -- cystic fibrosis -- lung lobe -- lung MRI -- neural network -- pediatrics; Nuclear magnetic resonance -- Periodicals; Electron paramagnetic resonance -- Periodicals; 616.07548
• DOI: 10.1002/mrm.29184
• Languages: English
• ISSNs: 0740-3194

Abstract

Abstract : Purpose: To introduce a widely applicable workflow for pulmonary lobe segmentation of MR images using a recurrent neural network (RNN) trained with chest CT datasets. The feasibility is demonstrated for 2D coronal ultrafast balanced SSFP (ufSSFP) MRI. Methods: Lung lobes of 250 publicly accessible CT datasets of adults were segmented with an open‐source CT‐specific algorithm. To match 2D ufSSFP MRI data of pediatric patients, both CT data and segmentations were translated into pseudo‐MR images that were masked to suppress anatomy outside the lung. Network‐1 was trained with pseudo‐MR images and lobe segmentations and then applied to 1000 masked ufSSFP images to predict lobe segmentations. These outputs were directly used as targets to train Network‐2 and Network‐3 with non‐masked ufSSFP data as inputs, as well as an additional whole‐lung mask as input for Network‐2. Network predictions were compared to reference manual lobe segmentations of ufSSFP data in 20 pediatric cystic fibrosis patients. Manual lobe segmentations were performed by splitting available whole‐lung segmentations into lobes. Results: Network‐1 was able to segment the lobes of ufSSFP images, and Network‐2 and Network‐3 further increased segmentation accuracy and robustness. The average all‐lobe Dice similarity coefficients were 95.0 ± 2.8 (mean ± pooled SD [%]) and 96.4 ± 2.5, 93.0 ± 2.0; and the average median Hausdorff distances were 6.1 ± 0.9 (mean ± SD [mm]), 5.3 ± 1.1, 7.1 ± 1.3 for Network‐1, Network‐2, and Network‐3, respectively. Conclusion: Recurrent neural network lung lobe segmentation of 2D ufSSFP imaging is feasible, in good agreement with manual segmentations. The proposed workflow might provide access to automated lobe segmentations for various lung MRI examinations and quantitative analyses.