Learning joint surface reconstruction and segmentation, from brain images to cortical surface parcellation.

Reconstructing and segmenting cortical surfaces from MRI is essential to a wide range of brain analyses. However, most approaches follow a multi-step slow process, such as a sequential spherical inflation and registration, which requires considerable computation times. To overcome the limitations arising from these multi-steps, we propose SegRecon, an integrated end-to-end deep learning method to jointly reconstruct and segment cortical surfaces directly from an MRI volume in one single step. We train a volume-based neural network to predict, for each voxel, the signed distances to multiple nested surfaces and their corresponding spherical representation in atlas space. This is, for instance, useful for jointly reconstructing and segmenting the white-to-gray-matter interface and the gray-matter-to-CSF (pial) surface. We evaluate the performance of our surface reconstruction and segmentation method with a comprehensive set of experiments on the MindBoggle, ABIDE and OASIS datasets. Our reconstruction error is found to be less than 0.52 mm and 0.97 mm in terms of average Hausdorff distance to the FreeSurfer generated surfaces. Likewise, the parcellation results show over 4% improvements in average Dice with respect to FreeSurfer, in addition to an observed drastic speed-up from hours to seconds of computation on a standard desktop station.