AFNI program: suma

Usage:  
 Mode 0: Just type suma to see some toy surface and play
         with the interface. Some surfaces are generated
         using T. Lewiner's MarchingCubes library. 
         Use '.' and ',' keys to cycle through surfaces.

 Mode 1: Using a spec file to specify surfaces
                suma -spec  
                     [-sv ] [-ah AfniHost]

   -spec : 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). 
                      The Spec file should be located in the directory 
                      containing the surfaces.
   [-sv ]: Anatomical volume used in creating the surface 
                    and registerd to the current experiment's anatomical 
                    volume (using @SUMA_AlignToExperiment). 
                    This parameter is optional, but linking to AFNI is 
                    not possible without it.If you find the need for it 
                    (as some have), you can specify the SurfVol in the 
                    specfile. You can do so by adding the field 
                    SurfaceVolume to each surface in the spec file. 
                    In this manner, you can have different surfaces using
                    different surface volumes.
   [-ah AfniHost]: Name (or IP address) of the computer running AFNI. 
                     This parameter is optional, the default is localhost.
                     When both AFNI and SUMA are on the same computer, 
                     communication is through shared memory. 
                     You can turn that off by explicitly setting AfniHost
                     to 127.0.0.1
   [-niml]: Start listening for NIML-formatted elements.
   [-dev]: Allow access to options that are not well polished for
           mass consuption.

 Mode 2: Using -t_TYPE or -t* options to specify surfaces on command line.
         -sv, -ah, -niml and -dev are still applicable here. This mode 
         is meant to simplify the quick viewing of a surface model.
                suma [-i_TYPE surface] [-t* surface] 
         Surfaces specified on command line are place in a group
         called 'DefGroup'.
         If you specify nothing on command line, you will have a random
         surface created for you. Some of these surfaces are generated
         using Thomas Lewiner's sample volumes for creating isosurfaces.
         See suma -sources for a complete reference.

 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.

 Modes 1 & 2: You can mix the two modes for loading surfaces but the -sv
              option may not be properly applied.
              If you mix these modes, you will have two groups of
              surfaces loaded into SUMA. You can switch between them
              using the 'Switch Group' button in the viewer controller.

   [-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.
 
   [-visuals] Shows the available glxvisuals and exits.
   [-version] Shows the current version number.
   [-environment] Shows a list of all environment variables, 
                  their default setting and your current setting.
                  The output can be used as a new .sumarc file.
                  Since it takes into consideration your own settings
                  this command can be used to update your .sumarc 
                  regularly with a csh command like this:
                  suma -environment > ~/sumarc && mv ~/sumarc ~/.sumarc
   [-latest_news] Shows the latest news for the current 
                  version of the entire SUMA package.
   [-all_latest_news] Shows the history of latest news.
   [-progs] Lists all the programs in the SUMA package.
   [-sources] Lists code sources used in parts of SUMA.
   [-help_nido] Help message for displayable objects of type NIDO

   For help on interacting with SUMA, press 'ctrl+h' with the mouse 
   pointer inside SUMA's window.

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

   ++ SUMA version 2006_7_3
New Programs:
  + SurfDsetInfo: Program to display surface dataset information.
  + AnalyzeTrace: Program to analyze the output of -trace option.
  + DriveSuma: Program to control SUMA from the command line
  + imcat: Program to catenate images.
  + Surf2VolCoord: Surface-node to voxel correspondence.
  + SurfDist: Program to calculate internodal distances.
  + SpharmDeco: Spherical harmonics decomposition.
  + SpharmReco: Spherical harmonics reconstruction.
Modifications:
  + SUMA:
    o Addition of new Displayable Objects (DO)(ctrl+Alt+s)
    o Allow replacement of pre-loaded DO and Dsets
    o Support for .niml.dset as format for surface-based anlysis
    o High resolution image saving with ctrl+r
    o Bug fixes for support of niml dset format
    o Use of '[i]' to select node index from surface dset
    o Scroll lists for I T and B selectors in SUMA
    o Graphing of dset content with 'g'
    o Display of text and images, see suma -help_nido 
  + SurfDist:
    o Output of node path along with shortest distance.
  + ConvertDset:
    o Output of full dsets if needed
  + ROIgrow:
    o Grows regions separately, depending on labels.
  + ROI2dataset:
    o outputs full datasets if needed.
  + SurfSmooth:
    o Improved HEAT_05 method.
    o New 'blurring to' a FWHM with HEAT_07 method.
  + SurfFWHM:
    o Estimating FWHM on the surface.
  + MapIcosahedron:
    o Better handling of surface centers. 

CVS tag:
   SUMA_2005_04_29_1733

Compile Date:
   Feb 12 2009



    Ziad S. Saad SSCC/NIMH/NIH saadz@mail.nih.gov