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: 

        Old Usage:
        ----------
        State name of spherical surface to which icosahedron 
        is inflated. Typical example for FreeSurfer surfaces would be 
        'sphere.reg', and that's the default used by the program. 

        New Usage:
        ----------
        State name or filename of spherical surface to which icosahedron 
        is inflated. Typical example for FreeSurfer surfaces would be 
        'sphere.reg', and that's the default used by the program. 
        Searching is first done assuming a State name and if that does
        not return exactly one match, a search based on the filename
        is carried out.

   The following four options affect the geometric center and radius
   settings of morphSurf. In previous versions, the geometric center
   was set to the center of mass. A better estimate of the geometric
   center is now obtained and this might make standard-mesh surfaces
   less sensitive to distortions in the spherical surfaces.
   With this change, the coordinates of the nodes will be silghtly
   different from in previous versions. If you insist on the old 
   method, use the option -use_com below.
   ----------------------------------------------------------------
   -sphere_at_origin: Geometric center of morphSurf sphere is at 
                      0.0 0.0 0.0. This is usually the case but
                      if you do not know, let the program guess.

   -sphere_center cx cy cz: Geometric center of morphSurf sphere. 
                            If not specified, it will be estimated.
      Note: It is best to specify cx cy cz or use -sphere_at_origin
            when the center is known.

   -use_com: (ONLY for backward compatibility)
             Use this option to make the center of mass of morpSurf.
             be the geometric center estimate. This is not optimal,
             use this option only for backward compatibility.
             The new results, i.e. without -use_com, should always be
             better.

   -sphere_radius R: Radius of morphSurf sphere. If not specified,
                     this would be the average radius of morpSurf.
                     
   ----------------------------------------------------------------

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

   -prefix FOUT: prefix for output files.
        (optional, default 'std.')

   -morph_sphere_check: Do some quality checks on morphSurf and exit.
                        This option now replaces -sph_check and -sphreg_check
                        See output of SurfQual -help for more info on this
                        option's output.

**********************************************
-sph_check and -sphreg_check are now OBSOLETE. 

   [-sph_check]:(OBSOLETE, use -morph_sphere_check instead) 
                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]: (OBSOLETE, use -morph_sphere_check instead)
                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.

**********************************************

   -all_surfs_spec: When specified, includes original-mesh surfaces 
       and icosahedron in output spec file.
       (optional, default does not include original-mesh surfaces)
   -verb: verbose.
   -write_nodemap: (default) Write a file showing the mapping of each 
                   node in the icosahedron to the closest
                   three nodes in the original mesh.
                   The file is named by the prefix FOUT
                   suffixed by MI.1D
  NOTE: This option is useful for understanding what contributed
        to a node's position in the standard meshes (STD_M).
        Say a triangle on the  STD_M version of the white matter
        surface (STD_WM) looks fishy, such as being large and 
        obtuse compared to other triangles in STD_M. Right
        click on that triangle and get one of its nodes (Ns)
        search for Ns in column 0 of the MI.1D file. The three
        integers (N0, N1, N2) on the same row as Ns will point 
        to the three nodes on the original meshes (sphere.reg) 
        to which Ns (from the icosahedron) was mapped. Go to N1
        (or N0 or N2) on the original sphere.reg and examine the
        mesh there, which is best seen in mesh view mode ('p' button).
        It will most likely be the case that the sphere.reg mesh
        there would be highly distorted (quite compressed).
   -no_nodemap: Opposite of write_nodemap

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 saadz@mail.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 2006_7_3

CVS tag:
   SUMA_2005_04_29_1733

Compile Date:
   Feb 12 2009


          Brenna D. Argall LBC/NIMH/NIH  
(contact) Ziad S. Saad     SSC/NIMH/NIH saadz@mail.nih.gov