AFNI program: SpharmReco

Spherical Harmonics Reconstruction from a set of harmonics 
and their corresponding coefficients.

Usage: 
  SpharmReco <-i_TYPE S> <-l L>
             <-bases_prefix BASES>
             <-coef BETA.0> <-coef BETA.1> ...
             [<-prefix PREFIX>] [<-o_TYPE SDR> ...]
             [-debug DBG]  [-sigma s]
Input:
  -i_TYPE SURF: SURF is a surface that is only used to provide
                the topology of the mesh (the nodes' connections)
  -l L: Decomposition order
  -bases_prefix BASES_PREFIX: Files containing the bases functions (spherical
                              harmonics). See SpharmDeco for generating these
                              files.
  -coef COEF.n: BETA.n is the coefficients file that is used to recompose 
                the nth data column. These files are created with SpharmDeco.
                You can specify N coefficient files by repeating the 
                option on command line. If N is a multiple 
                of three AND you use -o_TYPE option, then each three 
                consecutive files are considered to form the XYZ coordinates
                of a surface. See sample commands in @Spharm.examples 
  -prefix PREFIX: Write out the reconstructed data into dataset PREFIX. 
                  the output dataset contains N columns; one for each of the
                  COEF.n files.
  -o_TYPE SDR: Write out a new surface with reconstructed coordinates.
               This requires N to be a multiple of 3, so 6 -coef options
               will result in 2 surfaces written to disk. The naming of the
               surfaces depends on the number of -o_TYPE options used, much 
               like in SpharmDeco
  -debug DBG: Debug levels (1-3)
  -sigma s: Smoothing parameter (0 .. 0.001) which weighs down the 
            contribution of higher order harmonics.

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 For more detail, references, and examples, see script @Spharm.examples  
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 Specifying input surfaces using -i or -i_TYPE options: 
    -i_TYPE inSurf specifies the input surface,
            TYPE is one of the following:
       fs: FreeSurfer surface. 
           If surface name has .asc it is assumed to be
           in ASCII format. Otherwise it is assumed to be
           in BINARY_BE (Big Endian) format.
           Patches in Binary format cannot be read at the moment.
       sf: SureFit surface. 
           You must specify the .coord followed by the .topo file.
       vec (or 1D): Simple ascii matrix format. 
            You must specify the coord (NodeList) file followed by 
            the topo (FaceSetList) file.
            coord contains 3 floats per line, representing 
            X Y Z vertex coordinates.
            topo contains 3 ints per line, representing 
            v1 v2 v3 triangle vertices.
       ply: PLY format, ascii or binary.
            Only vertex and triangulation info is preserved.
       byu: BYU format, ascii.
            Polygons with more than 3 edges are turned into
            triangles.
       bv: BrainVoyager format. 
           Only vertex and triangulation info is preserved.
       dx: OpenDX ascii mesh format.
           Only vertex and triangulation info is preserved.
           Requires presence of 3 objects, the one of class 
           'field' should contain 2 components 'positions'
           and 'connections' that point to the two objects
           containing node coordinates and topology, respectively.
       gii: GIFTI XML surface format.
 Note that if the surface filename has the proper extension, 
 it is enough to use the -i option and let the programs guess
 the type from the extension.
 Specifying a surface specification (spec) file:
    -spec SPEC: specify the name of the SPEC file.
 Specifying output surfaces using -o or -o_TYPE options: 
    -o_TYPE outSurf specifies the output surface, 
            TYPE is one of the following:
       fs: FreeSurfer ascii surface. 
       fsp: FeeSurfer ascii patch surface. 
            In addition to outSurf, you need to specify
            the name of the parent surface for the patch.
            using the -ipar_TYPE option.
            This option is only for ConvertSurface 
       sf: SureFit surface. 
           For most programs, you are expected to specify prefix:
           i.e. -o_sf brain. In some programs, you are allowed to 
           specify both .coord and .topo file names: 
           i.e. -o_sf XYZ.coord TRI.topo
           The program will determine your choice by examining 
           the first character of the second parameter following
           -o_sf. If that character is a '-' then you have supplied
           a prefix and the program will generate the coord and topo names.
       vec (or 1D): Simple ascii matrix format. 
            For most programs, you are expected to specify prefix:
            i.e. -o_1D brain. In some programs, you are allowed to 
            specify both coord and topo file names: 
            i.e. -o_1D brain.1D.coord brain.1D.topo
            coord contains 3 floats per line, representing 
            X Y Z vertex coordinates.
            topo contains 3 ints per line, representing 
            v1 v2 v3 triangle vertices.
       ply: PLY format, ascii or binary.
       byu: BYU format, ascii or binary.
       gii: GIFTI format, ascii.
            You can also enforce the encoding of data arrays
            by using gii_asc, gii_b64, or gii_b64gz for 
            ASCII, Base64, or Base64 Gzipped. 
            If AFNI_NIML_TEXT_DATA environment variable is set to YES, the
            the default encoding is ASCII, otherwise it is Base64.
 Note that if the surface filename has the proper extension, 
 it is enough to use the -o option and let the programs guess
 the type from the extension.

  SUMA communication options:
      -talk_suma: Send progress with each iteration to SUMA.
      -refresh_rate rps: Maximum number of updates to SUMA per second.
                         The default is the maximum speed.
      -send_kth kth: Send the kth element to SUMA (default is 1).
                     This allows you to cut down on the number of elements
                     being sent to SUMA.
      -sh : Name (or IP address) of the computer running SUMA.
                      This parameter is optional, the default is 127.0.0.1 
      -ni_text: Use NI_TEXT_MODE for data transmission.
      -ni_binary: Use NI_BINARY_MODE for data transmission.
                  (default is ni_binary).
      -feed_afni: Send updates to AFNI via SUMA's talk.


   [-novolreg|-noxform]: Ignore any Rotate, Volreg, Tagalign, 
                or WarpDrive transformations present in 
                the Surface Volume.
  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 2006_7_3

CVS tag:
   SUMA_2005_04_29_1733

Compile Date:
   Jan 29 2009

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