AFNI program: @SUMA_Make_Spec_FS

@SUMA_Make_Spec_FS - prepare for surface viewing in SUMA

    This script goes through the following steps:
      - verify existence of necessary programs 
        (afni, to3d, suma, mris_convert)
      - determine the location of surface and COR files
      - creation of ascii surface files via 'mris_convert'
      - creation of left and right hemisphere SUMA spec files
      - creation of an AFNI dataset from the COR files via 'to3d'
      - creation of AFNI datasets from various .mgz volumes created
        by FreeSurfer. The segmentation volumes with aseg in the 
        name are best viewed in AFNI with the FreeSurfer_Seg_255
        colormap. See bottom of @SUMA_FSvolToBRIK -help for more
        info.

      - all created files are stored in a new SUMA directory

  Usage: @SUMA_Make_Spec_FS [options] -sid SUBJECT_ID

  examples:

    @SUMA_Make_Spec_FS -sid subject1
    @SUMA_Make_Spec_FS -help
    @SUMA_Make_Spec_FS -fspath subject1/surface_stuff -sid subject1
    @SUMA_Make_Spec_FS -neuro -sid 3.14159265 -debug 1

  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

    -fspath PATH    : path to 'surf' and 'orig' directories
          e.g. -fspath subject1/surface_info
          the default PATH value is './', the current directory

          This is generally the location of the 'surf' directory,
          though having PATH end in surf is OK.  The mri/orig
          directory should also be located here.

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

    -neuro          : use neurological orientation
          e.g. -neuro
          the default is radiological orientation

          In the default radiological orientation, the subject's
          right is on the left side of the image.  In the
          neurological orientation, left is really left.

    -sid SUBJECT_ID : required subject ID for file naming


  notes:

    1. Surface file names should look like 'lh.smoothwm'.
    2. Patches of surfaces need the word patch in their name, in
       order to use the correct option for 'mris_convert'.
    3. Flat surfaces must have .flat in their name.
    4. 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.

     R. Reynolds (rickr@codon.nih.gov)
     Z. Saad (saadz@mail.nih.gov)
     M. Beauchamp (Michael.S.Beauchamp@uth.tmc.edu)