We are one of the few groups in the world that can perform cortical thickness analysis on MRI scans from rodent brains. We have developed a fully-automated pipeline for computation of vertex-wise and region-of-interest (ROI)-based cortical thickness measures.

This schematic provides an overview of our proprietary processing pipeline. 

Using the cortical mantle as a mask (A), a Laplacian equation is used to identify the midline (B) and extend streamlines from this point to the inner and outer surfaces (C). The length of the streamline at each vertex (D) on the surface generates a measure of cortical thickness. The streamline lengths can then be averaged over specific cortical region, utilizing a surface atlas (E)  to generate regional mean thickness data (F).

Given that images from all mice are in the same coordinate space, the individual surfaces can also be averaged to generate mean thickness surface maps (G) for each group of mice, which can then be utilized to generate whole surface, groupwise statistical comparisons, such as t-statistic maps (H).