FreeSurferÕs automated topology fixer removes smaller topological defects.
From GUI: SubjectTools ˆ Fix Surface Topology
From Command Line:  fix_subject <subject_name>
 Class Example:  (from within lc_play/ directory)
fix_subject  lc_avg
orÉ recon-all  -stage3  -subjid lc_avg
Volume
preprocessing
Segmentation
Inflation
Manual Editing
Re-inflation
Fix topology
Final Surface
Volume/Surface
postprocessing
Cutting &
Flattening