A U-Net Deep Learning Framework for High Performance Vessel Segmentation in Patients With Cerebrovascular Disease

• Published in: Frontiers in neuroscience Vol. 13; p. 97
• Main Authors: Livne, Michelle, Rieger, Jana, Aydin, Orhun Utku, Taha, Abdel Aziz, Akay, Ela Marie, Kossen, Tabea, Sobesky, Jan, Kelleher, John D, Hildebrand, Kristian, Frey, Dietmar, Madai, Vince I
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Research Foundation 28-02-2019; Frontiers Media S.A
• Subjects: Automation; Brain research; cerebrovascular disease; Cerebrovascular diseases; Computer science; Cortex; Deep learning; Medical imaging; Neural networks; Neuroscience; Patients; Segmentation; Stroke; U-net; Veins & arteries; Austria; Germany; deep learning; segmentation; cerebrovascular disease; U-net; medical imaging
• ISSN: 1662-4548; 1662-453X; 1662-453X
• DOI: 10.3389/fnins.2019.00097

Brain vessel status is a promising biomarker for better prevention and treatment in cerebrovascular disease. However, classic rule-based vessel segmentation algorithms need to be hand-crafted and are insufficiently validated. A specialized deep learning method-the U-net-is a promising alternative. Using labeled data from 66 patients with cerebrovascular disease, the U-net framework was optimized and evaluated with three metrics: Dice coefficient, 95% Hausdorff distance (95HD) and average Hausdorff distance (AVD). The model performance was compared with the traditional segmentation method of graph-cuts. Training and reconstruction was performed using 2D patches. A full and a reduced architecture with less parameters were trained. We performed both quantitative and qualitative analyses. The U-net models yielded high performance for both the full and the reduced architecture: A Dice value of ~0.88, a 95HD of ~47 voxels and an AVD of ~0.4 voxels. The visual analysis revealed excellent performance in large vessels and sufficient performance in small vessels. Pathologies like cortical laminar necrosis and a rete mirabile led to limited segmentation performance in few patients. The U-net outperfomed the traditional graph-cuts method (Dice ~0.76, 95HD ~59, AVD ~1.97). Our work highly encourages the development of clinically applicable segmentation tools based on deep learning. Future works should focus on improved segmentation of small vessels and methodologies to deal with specific pathologies.