AFNI program: MapIcosahedron

Usage: MapIcosahedron <-spec specFile> 
                      [-rd recDepth] [-ld linDepth] 
                      [-morph morphSurf] 
                      [-it numIt] [-prefix fout] 
                      [-verb] [-help]

Creates new versions of the original-mesh surfaces using the mesh
of an icosahedron. 

   -spec specFile: spec file containing original-mesh surfaces
        including the spherical and warped spherical surfaces.

   -rd recDepth: recursive (binary) tesselation depth for icosahedron.
        (optional, default:3) See CreateIcosahedron for more info.

   -ld linDepth: number of edge divides for linear icosahedron tesselation 
        (optional, default uses binary tesselation).
        See CreateIcosahedron -help for more info.

   *Note: Enter -1 for recDepth or linDepth to let program 
          choose a depth that best approximates the number of nodes in
          original-mesh surfaces.

   -morph morphSurf: surface state to which icosahedron is inflated 
        accectable inputs are 'sphere.reg' and 'sphere'
        (optional, default uses sphere.reg over sphere).

   -it numIt: number of smoothing interations 
        (optional, default none).

   -prefix fout: prefix for output files.
        (optional, default MapIco)

   NOTE: See program SurfQual -help for more info on the following 2 options.
   [-sph_check]: Run tests for checking the spherical surface (sphere.asc)
                The program exits after the checks.
                This option is for debugging FreeSurfer surfaces only.

   [-sphreg_check]: Run tests for checking the spherical surface (sphere.reg.asc)
                The program exits after the checks.
                This option is for debugging FreeSurfer surfaces only.

   -sph_check and -sphreg_check are mutually exclusive.

   -verb: When specified, includes original-mesh surfaces 
       and icosahedron in output spec file.
       (optional, default does not include original-mesh surfaces)

NOTE 1: The algorithm used by this program is applicable
      to any surfaces warped to a spherical coordinate
      system. However for the moment, the interface for
      this algorithm only deals with FreeSurfer surfaces.
      This is only due to user demand and available test
      data. If you want to apply this algorithm using surfaces
      created by other programs such as SureFit and Caret, 
      Send ziad@nih.gov a note and some test data.

NOTE 2: At times, the standard-mesh surfaces are visibly
      distorted in some locations from the original surfaces.
      So far, this has only occurred when original spherical 
      surfaces had topological errors in them. 
      See SurfQual -help and SUMA's online documentation 
      for more detail.

++ SUMA version 2.5000, June 10 2004

Compile Date:
   Aug  3 2004


       Brenna D. Argall LBC/NIMH/NIH brenna.argall@nih.gov 
       Ziad S. Saad     SSC/NIMH/NIH ziad@nih.gov
          Fri Sept 20 2002