The standard FreeSurfer pipeline itself includes removal of non-brain tissue using a hybrid watershed/surface deformation procedure (58), automated Talairach transformation, segmentation of the subcortical white matter and deep gray matter volumetric structures including hippocampus, amygdala, caudate, putamen, and ventricles (49,50), intensity normalization (59), tessellation of the gray/white matter boundary, automated topology correction (48,57), and surface deformation following intensity gradients to place optimally the gray/white and gray/cerebrospinal fluid borders at the locations where the greatest shifts in intensity define the transitions between tissue classes (45-47). Once the cortical models were complete, a number of deformable procedures were performed including surface inflation (51), registration to a spherical atlas that utilized individual cortical folding patterns to match cortical geometry across subjects (52), parcellation of the cerebral cortex into units based on gyral and sulcal structure (53,60), and creation of a variety of surface based data maps. All automatically generated volumes and maps were inspected visually for accuracy, and manual corrections using FreeSurfer tools were carried out as needed.
