Automated reconstruction of the cerebral cortex in multiple sclerosis patients

Although cortical atrophy in multiple sclerosis (MS) has been reported in the literature, most cortical reconstruction techniques do not account for lesions. In this work, we propose an automated pipeline for cortical reconstruction from magnetic resonance brain images with MS lesions. The pipeline extends previously well validated methods to allow for the presence of lesions and to accommodate multichannel imaging. We validate this approach on simulated and real images. Application of the pipeline to 103 MS brains produces thickness measurements that agree well with the literature.