Wagstyl K., Lerch JP.
© 2018, Springer Science+Business Media, LLC. Multiple studies have measured cortical thickness from MRI since the advent of high contrast and 1 mm3 resolution anatomical acquisitions and the development of advanced image processing algorithms. In this chapter we provide an overview of the methods for extracting cortical thickness, focusing on the two dominant packages in the field, FreeSurfer and CIVET. In addition, we review the confounds and artifacts that can bedevil cortical thickness studies. Lastly, we describe the potential of inferring microstructural changes based on the mesoscopic measurements acquired from standard structural acquisitions.