Usage:    CompareSurfaces
             -spec <Spec file>
             -hemi <L or R>
             -sv1 <volparentaligned1.BRIK>
             -sv2 <volparentaligned2.BRIK>
             [-prefix <fileprefix>]

   NOTE: This program is now superseded by SurfToSurf

   This program calculates the distance, at each node in Surface 1 (S1) to Surface 2 (S2)
   The distances are computed along the local surface normal at each node in S1.
   S1 and S2 are the first and second surfaces encountered in the spec file, respectively.

   -spec <Spec file>: File containing surface specification. This file is typically
                      generated by @SUMA_Make_Spec_FS (for FreeSurfer surfaces) or
                      @SUMA_Make_Spec_SF (for SureFit surfaces).
   -hemi <left or right>: specify the hemisphere being processed
   -sv1 <volume parent BRIK>:volume parent BRIK for first surface
   -sv2 <volume parent BRIK>:volume parent BRIK for second surface

Optional parameters:
   [-prefix <fileprefix>]: Prefix for distance and node color output files.
                           Existing file will not be overwritten.
   [-onenode <index>]: output results for node index only.
                       This option is for debugging.
   [-noderange <istart> <istop>]: output results from node istart to node istop only.
                                  This option is for debugging.
   NOTE: -noderange and -onenode are mutually exclusive
   [-nocons]: Skip mesh orientation consistency check.
              This speeds up the start time so it is useful
              for debugging runs.

   [-novolreg]: Ignore any Rotate, Volreg, Tagalign,
                or WarpDrive transformations present in
                the Surface Volume.
   [-noxform]: Same as -novolreg
   [-setenv "'ENVname=ENVvalue'"]: Set environment variable ENVname
                to be ENVvalue. Quotes are necessary.
             Example: suma -setenv "'SUMA_BackgroundColor = 1 0 1'"
                See also options -update_env, -environment, etc
                in the output of 'suma -help'
  Common Debugging Options:
   [-trace]: Turns on In/Out debug and Memory tracing.
             For speeding up the tracing log, I recommend
             you redirect stdout to a file when using this option.
             For example, if you were running suma you would use:
             suma -spec lh.spec -sv ... > TraceFile
             This option replaces the old -iodbg and -memdbg.
   [-TRACE]: Turns on extreme tracing.
   [-nomall]: Turn off memory tracing.
   [-yesmall]: Turn on memory tracing (default).
  NOTE: For programs that output results to stdout
    (that is to your shell/screen), the debugging info
    might get mixed up with your results.

Global Options (available to all AFNI/SUMA programs)
  -h: Mini help, at time, same as -help in many cases.
  -help: The entire help output
  -HELP: Extreme help, same as -help in majority of cases.
  -h_view: Open help in text editor. AFNI will try to find a GUI editor
  -hview : on your machine. You can control which it should use by
           setting environment variable AFNI_GUI_EDITOR.
  -h_web: Open help in web browser. AFNI will try to find a browser.
  -hweb : on your machine. You can control which it should use by
          setting environment variable AFNI_GUI_EDITOR.
  -h_find WORD: Look for lines in this programs's -help output that match
                (approximately) WORD.
  -h_raw: Help string unedited
  -h_spx: Help string in sphinx loveliness, but do not try to autoformat
  -h_aspx: Help string in sphinx with autoformatting of options, etc.
  -all_opts: Try to identify all options for the program from the
             output of its -help option. Some options might be missed
             and others misidentified. Use this output for hints only.

   For more help:

   If you can't get help here, please get help somewhere.

Compile Date:
   Oct 13 2022

    Shruti Japee LBC/NIMH/NIH Ziad S. Saad SSSC/NIMH/NIH