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 The Tools -> Process Volume menu item starts a
 four-part background process to prepare the 3-D
 MRI data to make a surface.
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[old Linux-only FreeSurfer0.8]

(1) Normalize Intensities

The output files written by this procedure are:

 images: $SUBJECTS_DIR/$name/mri/T1/COR-???

(2) Compute Talairach (uses MINC tools)

 xform: $SUBJECTS_DIR/$name/mri/transforms/
                                 talairach.xfm
(3) Strip Skull

A subtessellated icosahedron is expanded shrunk
to reach the surface of the brain using the
normalized data set.  At each point on the
surface a 'core sample' is used to search for the
first black lamina that corresponds to the inner
surface of the inner table of bone in a
T1-weighted scan, while at the same time,
preserving neighbor relations.  Once this surface
is found, it is used to strip the skull off of
the T1 data set.  The output files written by
this procedure are:

 shrinksurf: $SUBJECTS_DIR/$name/bem/brain.tri
 images: $SUBJECTS_DIR/$name/mri/brain/COR-???

Inspect this output to see that no gyri have
been trimmed.  If they have, open Preferences ->
Expert Preferences => RmSkull tab, reduce fzero
and increase fmax, and re-run.

(4) White Matter Filter

An oriented filter is applied to the stripped
data set to 'floss' and 'spackle' small defects.
Filter coefficients are computed for each 5x5x5
volume in order to determine which plane is most
likely to be parallel ot the cortical surface,
and then a modified median filter is applied.
The output files written by this procedure are:

 images: $SUBJECTS_DIR/$name/mri/wm/COR-???
