FreeSurfer Processing & Editing Overview

FreeSurfer processing and editing overview. Description of basic processing, command line operation, and step-by-step guide to manual edits (control points, white-matter edits, pial edits). This was initially made for as a training tool regarding FreeSurfer workflow at the Wig Neuroimaging Laboratory, but examples of artifacts/errors and how to fix them using manual edits should be applicable to any FreeSurfer data.

The current version of the manual (v2.1) is an update to the original manual that was referenced in Savalia et al. (2017) Human Brain Mapping (FREESURFER Processing & editing overview – prepared by the Cognitive Neuroimaging Laboratory; October 2015). The updates include reducing lab-specific settings, additional details regarding cerebellum edits, and some updates based on newer versions of FreeSurfer/FreeView.