Critical Analysis of NeuroAnatomical Software Protocols Reveals Clinically Relevant Differences in Parcellation Schemes

high replicability in region-of-interest (ROI) morphometric or ROI-based connectivity analyses is essential for such methods to provide biomarkers of good health or disease. In this article, we focus on package design, and more specifically on cortical parcellation protocols, for novel insight into their contribution to inter-package differences. A critical analysis of cortical parcellation protocols from FreeSurfer, BrainSuite, BrainVISA and BrainGyrusMapping revealed major limitations. Details of reference populations are generally missing, cortical variability is not always explicitly accounted for and, more importantly, definition of gyral borders can be inconsistent. We recommend that in the package selection process end users incorporate protocol suitability for the ROIs under investigation, with these particular points in mind, as inter-package differences are likely to be significant and the source of incompatibility between studies' results.