AFNI program: @SUMA_Make_Spec_Caret

@SUMA_Make_Spec_Caret - prepare for surface viewing in SUMA

    This script was tested with Caret-5.2 surfaces.

    This script goes through the following steps:
      - determine the location of surfaces and 
        then AFNI volume data sets used to create them.
      - creation of left and right hemisphere SUMA spec files

      - all created files are stored in the directory where 
        surfaces are encountered

  Usage: @SUMA_Make_Spec_Caret [options] -sid SUBJECT_ID

  examples:

    @SUMA_Make_Spec_Caret -sid subject1
    @SUMA_Make_Spec_Caret -help
    @SUMA_Make_Spec_Caret -sfpath subject1/surface_stuff -sid subject1

  options:

    -help    : show this help information

    -debug LEVEL    : print debug information along the way
          e.g. -debug 1
          the default level is 0, max is 2

    -sfpath PATH    : path to directory containing 'SURFACES'
                      and AFNI volume used in creating the surfaces.
          e.g. -sfpath subject1/surface_models
          the default PATH value is './', the current directory

          This is generally the location of the 'SURFACES' directory,
          though having PATH end in SURFACES is OK.  

          Note: when this option is provided, all file/path
          messages will be with respect to this directory.


    -sid SUBJECT_ID : required subject ID for file naming


  notes:

    1. Surface file names should look like the standard names used by Caret:
       Human.3dAnatomy.LR.Fiducial.2006-05-09.54773.coord
       Human.3dAnatomy.LR.CLOSED.2006-05-09.54773.topo
       Otherwise the script cannot detect them. You will need to decide which
       surface is the most recent (the best) and the script helps you by listing
       the available surfaces with the most recent one first.
       This sorting ususally works except when the time stamps on the surface files
       are messed up. In such a case you just need to know which one to use.
       Once the Fiducial surface is chosen, it's complimentary surfaces are selected
       using the node number in the file name.
    3. You can tailor the script to your needs. Just make sure you rename it or risk
       having your modifications overwritten with the next SUMA version you install.
    4. The script looks for Fiducial Raw VeryInflated Inflated
       surfaces, let us know if more need to be sought.
    5. The test data I had contained .R. and .LR. surfaces! I am not sure what .LR.
       means since the surfaces are for one hemisphere but the script will use
       these surfaces too.

     R. Reynolds (rickr@codon.nih.gov), Z. Saad (saadz@mail.nih.gov)