Automated Brain Extraction from T1-weighted MRI of Rhesus Macaques using a U-Net Deep Learning Framework
Anqi Zhang, Donghoon Kim, Jeong-chul Kim, Brad A. Hobson, Sonny R. Elizaldi, John H. Morrison, Smita Swaminathan Iyer, Abhijit J. Chaudhari, Youngkyoo Jung · Proceedings on CD-ROM - International Society for Magnetic Resonance in Medicine. Scientific Meeting and Exhibition/Proceedings of the International Society for Magnetic Resonance in Medicine, Scientific Meeting and Exhibition · 2023
Transfer learning of an advanced deep learning framework, utilizing 3D U-Net pre-trained model, and trained on human brain MRI scans is proposed for brain extraction from MRI of other species. The proposed network architecture successfully performed whole brain extraction from rhesus macaque brain MRIs automatically with high accuracy, reduced errors, and lower computational cost. Options for data augmentation and different learning rates were also tested. Successful implementation of automated brain extraction would offer the potential to apply the same strategy on other animal models.