Structural Brain Volumetry Using FreeSurfer

The FreeSurfer (version 5.1.0) pipeline was used to generate cortical and subcortical volumetric measures (Dale et al., 1999 (link); Fischl et al., 1999 (link)). Estimated Total Intracranial Volume (eTIV) generated by FreeSurfer was used as an estimate for ICV in this study. The eTIV measure from FreeSurfer is in good agreement with ICV reference segmentation acquired from proton density weighted images) (Nordenskjöld et al., 2013 (link)) and has previously been used in several studies for normalization (Westman et al., 2011 (link), 2012 (link), 2013 (link)). The pipeline generated 68 cortical volumes (34 from each hemisphere) and 46 subcortical volumes. Volumes of white matter hypointensities, optic chiasm, right and left vessel, and left and right choroid plexus were excluded from further analysis. Cortical and subcortical volumetric measures from the right and left side were averaged (Walhovd et al., 2011 (link); Westman et al., 2013 (link)). In total 34 regional cortical volumes and 17 subcortical volumes were used for final analysis in the study. Image processing steps were visually inspected (skull-stripping errors and gray/white matter boundary) to ensure they had been carried out correctly.