AFNI program: SurfToSurf

Usage: SurfToSurf <-i_TYPE S1> [<-sv SV1>]
                  <-i_TYPE S2> [<-sv SV1>]
                  [<-prefix PREFIX>]
                  [<-output_params PARAM_LIST>]
                  [<-node_indices NODE_INDICES>]
                  [<-proj_dir PROJ_DIR>]
                  [<-data DATA>]
                  [<-node_debug NODE>]
                  [<-debug DBG_LEVEL>]
                  [-make_consistent]
 
  This program is used to interpolate data from one surface (S2)
 to another (S1), assuming the surfaces are quite similar in
 shape but having different meshes (non-isotopic).
 This is done by projecting each node (nj) of S1 along the normal
 at nj and finding the closest triangle t of S2 that is intersected
 by this projection. Projection is actually bidirectional.
 If such a triangle t is found, the nodes (of S2) forming it are 
 considered to be the neighbors of nj.
 Values (arbitrary data, or coordinates) at these neighboring nodes
 are then transfered to nj using barycentric interpolation or 
 nearest-node interpolation.
 Nodes whose projections fail to intersect triangles in S2 are given
 nonsensical values of -1 and 0.0 in the output.

 Mandatory input:
  Two surfaces are required at input. See -i_TYPE options
  below for more information. 

 Optional input:
  -prefix PREFIX: Specify the prefix of the output file.
                  The output file is in 1D format at the moment.
                  Default is SurfToSurf
  -output_params PARAM_LIST: Specify the list of mapping
                             parameters to include in output
     PARAM_LIST can have any or all of the following:
        NearestTriangleNodes: Use Barycentric interpolation (default)
                              and output indices of 3 nodes from S2
                              that neighbor nj of S1
        NearestNode: Use only the closest node from S2 (of the three 
                     closest neighbors) to nj of S1 for interpolation
                     and output the index of that closest node.
        NearestTriangle: Output index of triangle t from S2 that
                         is the closest to nj along its projection
                         direction. 
        DistanceToSurf: Output distance (signed) from nj, along 
                        projection direction to S2.
                        This is the parameter output by the precursor
                        program CompareSurfaces
        ProjectionOnSurf: Output coordinates of projection of nj onto 
                          triangle t of S2.
        Data: Output the data from S2, interpolated onto S1
              If no data is specified via the -data option, then
              the XYZ coordinates of SO2's nodes are considered
              the data.
  -data DATA: 1D file containing data to be interpolated.
              Each row i contains data for node i of S2.
              You must have one row for each node making up S2.
              In other terms, if S2 has N nodes, you need N rows
              in DATA. 
              Each column of DATA is processed separately (think
              sub-bricks, and spatial interpolation).
              You can use [] selectors to choose a subset 
              of columns.
              If -data option is not specified and Data is in PARAM_LIST
              then the XYZ coordinates of SO2's nodes are the data.
  -node_indices NODE_INDICES: 1D file containing the indices of S1
                              to consider. The default is all of the
                              nodes in S1. Only one column of values is
                              allowed here, use [] selectors to choose
                              the column of node indices if NODE_INDICES
                              has multiple columns in it.
  -proj_dir PROJ_DIR: 1D file containing projection directions to use
                      instead of the node normals of S1.
                      Each row should contain one direction for each
                      of the nodes forming S1.
  -make_consistent: Force a consistency check and correct triangle 
                    orientation of S1 if needed. Triangles are also
                    oriented such that the majority of normals point
                    away from center of surface.
                    The program might not succeed in repairing some
                    meshes with inconsistent orientation.

 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 surfaces using -t* options: 
   -tn TYPE NAME: specify surface type and name.
                  See below for help on the parameters.
   -tsn TYPE STATE NAME: specify surface type state and name.
        TYPE: Choose from the following (case sensitive):
           1D: 1D format
           FS: FreeSurfer ascii format
           PLY: ply format
           BYU: byu format
           SF: Caret/SureFit format
           BV: BrainVoyager format
           GII: GIFTI format
        NAME: Name of surface file. 
           For SF and 1D formats, NAME is composed of two names
           the coord file followed by the topo file
        STATE: State of the surface.
           Default is S1, S2.... for each surface.
 Specifying a Surface Volume:
    -sv SurfaceVolume [VolParam for sf surfaces]
       If you supply a surface volume, the coordinates of the input surface.
        are modified to SUMA's convention and aligned with SurfaceVolume.
        You must also specify a VolParam file for SureFit surfaces.
 Specifying a surface specification (spec) file:
    -spec SPEC: specify the name of the SPEC file.
 Specifying a surface using -surf_? method:
    -surf_A SURFACE: specify the name of the first
            surface to load. If the program requires
            or allows multiple surfaces, use -surf_B
            ... -surf_Z .
            You need not use _A if only one surface is
            expected.
            SURFACE is the name of the surface as specified
            in the SPEC file. The use of -surf_ option 
            requires the use of -spec option.
 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.
   [-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 saadz@mail.nih.gov     
       Shruti Japee LBC/NIMH/NIH  shruti@codon.nih.gov