Simulating Realistic MRI variations to Improve Deep Learning model and visual explanations using GradCAM

In the medical field, landmark detection in MRI plays an important role in reducing medical technician efforts in tasks like scan planning, image registration, etc. First, 88 landmarks spread across the brain anatomy in the three respective views -- sagittal, coronal, and axial are manually annotated, later guidelines from the expert clinical technicians are taken sub-anatomy-wise, for better localization of the existing landmarks, in order to identify and locate the important atlas landmarks even in oblique scans. To overcome limited data availability, we implement realistic data augmentation to generate synthetic 3D volumetric data. We use a modified HighRes3DNet model for solving brain MRI volumetric landmark detection problem. In order to visually explain our trained model on unseen data, and discern a stronger model from a weaker model, we implement Gradient-weighted Class Activation Mapping (Grad-CAM) which produces a coarse localization map highlighting the regions the model is focusing. Our experiments show that the proposed method shows favorable results, and the overall pipeline can be extended to a variable number of landmarks and other anatomies.