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 The Tools -> Fix Topology menu item starts a
 four-part background process to create the left
 and right hemisphere cortical surfaces
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[old Linux-only FreeSurfer0.8]

(1) Quick Sphere Right Hemisphere Surface
(2) Quick Sphere Left Hemisphere Surface

Inflate each hemisphere to an area-preserving
sphere to identify topological defects.  The
output files are:

 outsurf: $SUBJECTS_DIR/$name/surf/rh.qsphere
 outsurf: $SUBJECTS_DIR/$name/surf/lh.qsphere

(3) Fix Topology Right Sphere'd Surface
(4) Fix Topology Left Sphere'd Surface

Remove defects by finding sphere locations that
have more than one layer (e.g., a "handle" or
"wormhole").  Then, cut out these defects and
re-tessellate them.  The output files are:

 surface: $SUBJECTS_DIR/$name/surf/rh.orig
 surface: $SUBJECTS_DIR/$name/surf/lh.orig

These overwrite the originally reconstructed
surfaces.

(5) Re-Smooth Right Hemisphere White Matter
(6) Re-Smooth Left Hemisphere White Matter

The reconstructed white matter surface of the
right and left hemispheres is smoothed.  The
output files written by this procedure are:

 surface: $SUBJECTS_DIR/$name/surf/rh.smoothwm
 surface: $SUBJECTS_DIR/$name/surf/lh.smoothwm

(7) Re-Inflate Right Hemisphere
(8) Re-Inflate Left Hemisphere

Inflate the right and left hemisphere surfaces
while attempting to preserve local angles and
area.  The output files written by this procedure
are:

 surface: $SUBJECTS_DIR/$name/surf/rh.inflated
 surface: $SUBJECTS_DIR/$name/surf/lh.inflated

