Our team has developed an entire software platform for processing and analysis of MRI scans of rodent brains. Our methods are automated and do not require any manual measurements or corrections.

Briefly, all native anatomical MRI scans are spatially normalized to a standardized anatomical coordinate space. The individual, preprocessed images are linearly and non-linearly registered to an anatomical template. An atlas with predefined neuroanatomical structures is then applied, allowing for regional volumetric measures. We also apply a cortical mask, which is used for thickness analysis, as described on the next page.