AFNI program: SurfPatch

Usage:
  SurfPatch <-spec SpecFile> <-surf_A insurf> <-surf_B insurf> ...
            <-input nodefile inode ilabel> <-prefix outpref>  
            [-hits min_hits] [-masklabel msk] [-vol]

Usage 1:
  The program creates a patch of surface formed by nodes 
  in nodefile.
  Mandatory parameters:
     -spec SpecFile: Spec file containing input surfaces.
     -surf_X: Name of input surface X where X is a character
              from A to Z. If surfaces are specified using two
              files, use the name of the node coordinate file.
     -input nodefile inode ilabel: 
            nodefile is the file containing nodes defining the patch.
            inode is the index of the column containing the nodes
            ilabel is the index of the column containing labels of
                   the nodes in column inode. If you want to use
                   all the nodes in column indode, then set this 
                   parameter to -1 (default). 
                   If ilabel is not equal to 0 then the corresponding 
                   node is used in creating the patch.
                   See -masklabel option for one more variant.
     -prefix outpref: Prefix of output patch. If more than one surface
                      are entered, then the prefix will have _X added
                      to it, where X is a character from A to Z.
  Optional parameters:
     -hits min_hits: Minimum number of nodes specified for a triangle
                     to be made a part of the patch (1 <= min_hits <= 3)
                     default is 2.
     -masklabel msk: If specified, then only nodes that are labeled with
                     with msk are considered for the patch.
                     This option is useful if you have an ROI dataset file
                     and whish to create a patch from one out of many ROIs
                     in that file. This option must be used with ilabel 
                     specified (not = -1)

Usage 2:
  The program can also be used calculate between the same patch
  on two isotopic surfaces. See -vol option below.
      -vol: Calculate the volume formed by the patch on surf_A and
            and surf_B. For this option, you must specify two and
            only two surfaces with surf_A and surf_B options.
      -vol_only: Only calculate the volume, don't write out patches.

  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.
 

++ SUMA version 2.5000, June 10 2004

Compile Date:
   Aug  3 2004

       Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov