VINNA for Neonates -- Orientation Independence through Latent Augmentations

Abstract: Fast and accurate segmentation of neonatal brain images is highly desired to better understand and detect changes during development and disease. Yet, the limited availability of ground truth datasets, lack of standardized acquisition protocols, and wide variations of head positioning pose challenges for method development. A few automated image analysis pipelines exist for newborn brain MRI segmentation, but they often rely on time-consuming procedures and require resampling to a common resolution, subject to loss of information due to interpolation and down-sampling. Without registration and image resampling, variations with respect to head positions and voxel resolutions have to be addressed differently. In deep-learning, external augmentations are traditionally used to artificially expand the representation of spatial variability, increasing the training dataset size and robustness. However, these transformations in the image space still require resampling, reducing accuracy specifically in the context of label interpolation. We recently introduced the concept of resolution-independence with the Voxel-size Independent Neural Network framework, VINN. Here, we extend this concept by additionally shifting all rigid-transforms into the network architecture with a four degree of freedom (4-DOF) transform module, enabling resolution-aware internal augmentations (VINNA). In this work we show that VINNA (i) significantly outperforms state-of-the-art external augmentation approaches, (ii) effectively addresses the head variations present specifically in newborn datasets, and (iii) retains high segmentation accuracy across a range of resolutions (0.5-1.0 mm). The 4-DOF transform module is a powerful, general approach to implement spatial augmentation without requiring image or label interpolation. The specific network application to newborns will be made publicly available as VINNA4neonates.