A Double-Stage 3D U-Net for On-Cloud Brain Extraction and Multi-Structure Segmentation from 7T MR Volumes

The brain is the organ most studied using Magnetic Resonance (MR). The emergence of 7T scanners has increased MR imaging resolution to a sub-millimeter level. However, there is a lack of automatic segmentation techniques for 7T MR volumes. This research aims to develop a novel deep learning-based algorithm for on-cloud brain extraction and multi-structure segmentation from unenhanced 7T MR volumes. To this aim, a double-stage 3D U-Net was implemented in a cloud service, directing its first stage to the automatic extraction of the brain and its second stage to the automatic segmentation of the grey matter, basal ganglia, white matter, ventricles, cerebellum, and brain stem. The training was performed on the 90% (the 10% of which served for validation) and the test on the 10% of the Glasgow database. A mean test Dice Similarity Coefficient (DSC) of 96.33% was achieved for the brain class. Mean test DSCs of 90.24%, 87.55%, 93.82%, 85.77%, 91.53%, and 89.95% were achieved for the brain structure classes, respectively. Therefore, the proposed double-stage 3D U-Net is effective in brain extraction and multi-structure segmentation from 7T MR volumes without any preprocessing and training data augmentation strategy while ensuring its machine-independent reproducibility.