Cortical surface registration and parcellation are two essential steps in neuroimaging analysis. Conventionally, they are performed independently as two tasks, ignoring the inherent connections of these two closely-related tasks. Essentially, both tasks rely on meaningful cortical feature representations, so they can be jointly optimized by learning shared useful cortical features. To this end, we propose a deep learning framework for joint cortical surface registration and parcellation. Specifically, our approach leverages the spherical topology of cortical surfaces and uses a spherical network as the shared encoder to first learn shared features for both tasks. Then we train two task-specific decoders for registration and parcellation, respectively. We further exploit the more explicit connection between them by incorporating the novel parcellation map similarity loss to enforce the boundary consistency of regions, thereby providing extra supervision for the registration task. Conversely, parcellation network training also benefits from the registration, which provides a large amount of augmented data by warping one surface with manual parcellation map to another surface, especially when only few manually-labeled surfaces are available. Experiments on a dataset with more than 600 cortical surfaces show that our approach achieves large improvements on both parcellation and registration accuracy (over separately trained networks) and enables training high-quality parcellation and registration models using much fewer labeled data.
Keywords: Deep Neural Network; Parcellation; Surface Registration.