FreeSurfer is open source software used to process and analyze magnetic resonance imaging of the human brain. It is a convenient tool that helps elucidate various structural characteristics the brain. In this review, we introduce the various structural indices of the brain, analyzed using FreeSurfer and magnetoencephalography, which can evaluate neural activity with high temporal and spatial resolution. We consider that the FreeSurfer has great potential as a platform for multimodal neuroimaging studies.