FAST-AID Brain: Fast and Accurate Segmentation Tool using Artificial Intelligence Developed for Brain

Medical images used in clinical practice are heterogeneous and not the same quality as scans studied in academic research. Preprocessing breaks down in extreme cases when anatomy, artifacts, or imaging parameters are unusual or protocols are different. Methods robust to these variations are most needed. A novel deep learning method is proposed for fast and accurate segmentation of the human brain into 132 regions. The proposed model uses an efficient U-Net-like network and benefits from the intersection points of different views and hierarchical relations for the fusion of the orthogonal 2D planes and brain labels during the end-to-end training. Weakly supervised learning is deployed to take the advantage of partially labeled data for the whole brain segmentation and estimation of the intracranial volume (ICV). Moreover, data augmentation is used to expand the magnetic resonance imaging (MRI) data by generating realistic brain scans with high variability for robust training of the model while preserving data privacy. The proposed method can be applied to brain MRI data including skull or any other artifacts without preprocessing the images or a drop in performance. Several experiments using different atlases are conducted to evaluate the segmentation performance of the trained model compared to the state-of-the-art, and the results show higher segmentation accuracy and robustness of the proposed model compared to the existing methods across different intra- and inter-domain datasets.