The following sequence of steps results in a cortical gray and white surface:

All .pl scripts model files are in:

          ~david/Surface_deformation


The executables are in (for some there are two versions, one in each of the
following directories):

          ~david/public_bin/IRIX_6
          ~david/public_bin

                 print_n_polygons
                 new_fit_3d
                 set_object_colour
                 subdivide_polygons
                 measure_surface_area
                 mask_volume
                 box_filter_volume_nd
                 create_anchor_constraints
                 surface_mask2

The objects referred to are:

    /nil/david/Surface_deformation/white_model_320.obj
    /nil/david/Surface_deformation/white_matter_mask.obj
    /nil/david/Object_models/ellipsoid_{320,1280,5120,20480,81920}.obj.gz

----------------------------------------------------------------------------
To extract the left or right hemisphere only:

    Note that there are two places in the following instructions where you
must place an extra argument on the line, if you wish to extract the left or
right hemisphere.
----------------------------------------------------------------------------


---------------------------------------------------------------------------
  Step 0:   Set up
---------------------------------------------------------------------------

cd ~david/Surface_deformation

set path = ($path ~david/public_bin)          #   if not on an Origin
       OR
set path = ($path ~david/public_bin/IRIX_6)   #   if on an Origin

---------------------------------------------------------------------------
  Step 1:   1/2 hour   Creating a mask surface to chop of non-cortical white
                       matter
---------------------------------------------------------------------------

mask_cortical_white_matter.pl  in_classified.mnc  white_mask.obj  2.5

        or if you want one or the other hemisphere only:

mask_cortical_white_matter.pl  in_classified.mnc  white_mask.obj  2.5 ~david/Surface_deformation/left_hemisphere_model.obj

mask_cortical_white_matter.pl  in_classified.mnc  white_mask.obj  2.5 ~david/Surface_deformation/right_hemisphere_model.obj

---------------------------------------------------------------------------
  Step 2:   2 minutes  Masking the classified volume with the white_mask
---------------------------------------------------------------------------

surface_mask2  in_classified.mnc  white_mask.obj  white_masked.mnc
mask_volume    white_masked.mnc    white_masked.mnc    white_masked.mnc 1 2.5 0

---------------------------------------------------------------------------
  Step 3:   20 hours   Shrink wrapping a sphere to the MASKED white matter
                       matter,  (note that the second argument below is a
                                 prefix)
                       creating white_surface_{320,1280,5120,20480,81920}.obj
                       you can delete the model files that are created:
                            white_surface_m_{320,1280,5120,20480,81920}.obj
---------------------------------------------------------------------------

extract_white_surface.pl  white_masked.mnc   white_surface  2.5

                   or if you want the left or right hemisphere only

extract_white_surface.pl  white_masked.mnc   white_surface  2.5  ~david/Surface_deformation/left_white_model_320.obj
extract_white_surface.pl  white_masked.mnc   white_surface  2.5  ~david/Surface_deformation/right_white_model_320.obj

---------------------------------------------------------------------------
  Step 4:   10 hours   Expand a copy of the white surface out to the gray
                       boundary.  Note that now we can delete the temporary
                       masked white matter (white_masked.mnc), and use the
                       original classified volume for this step.
---------------------------------------------------------------------------

expand_from_white.pl  in_classified.mnc   white_surface_81920.obj  \
                      gray_surface_81920.obj  1.5