AFNI program: SurfQual

Usage: A program to check the quality of surfaces.
  SurfQual <-spec SpecFile> <-surf_A insurf> <-surf_B insurf> ...
             <-sphere> [-self_intersect] [-prefix OUTPREF]  

  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.
  Mesh winding consistency and 2-manifold checks are performed
  on all surfaces.
  Optional parameters:
     -summary: Provide summary of results to stdout
     -self_intersect: Check if surface is self intersecting.
                      This option is rather slow, so be patient.
                      In the presence of intersections, the output file
                      OUTPREF_IntersNodes.1D.dset will contain the indices
                      of nodes forming segments that intersect the surface.
  Most other checks are specific to spherical surfaces (see option below).
     -sphere: Indicates that surfaces read are spherical.
              With this option you get the following output.
              - Absolute deviation between the distance (d) of each
                node from the surface's center and the estimated
                radius(r). The distances, abs (d - r), are 
                and written to the file OUTPREF_Dist.1D.dset .
                The first column represents node index and the 
                second is the absolute distance. A colorized 
                version of the distances is written to the file 
                OUTPREF_Dist.1D.col (node index followed 
                by r g b values). A list of the 10 largest absolute
                distances is also output to the screen.
              - Also computed is the cosine of the angle between 
                the normal at a node and the direction vector formed
                formed by the center and that node. Since both vectors
                are normalized, the cosine of the angle is the dot product.
                On a sphere, the abs(dot product) should be 1 or pretty 
                close. Nodes where abs(dot product) < 0.9 are flagged as
                bad and written out to the file OUTPREF_BadNodes.1D.dset .
                The file OUTPREF_dotprod.1D.dset contains the dot product 
                values for all the nodes. The files with colorized results
                are OUTPREF_BadNodes.1D.col and OUTPREF_dotprod.1D.col .
                A list of the bad nodes is also output to the screen for
                convenience. You can use the 'j' option in SUMA to have
                the cross-hair go to a particular node. Use 'Alt+l' to
                have the surface rotate and place the cross-hair at the
                center of your screen.
              NOTE: For detecting topological problems with spherical
                surfaces, I find the dot product method to work best.
  Optional parameters:
     -prefix OUTPREF: Prefix of output files. 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.
                      THIS PROGRAM WILL OVERWRITE EXISTING FILES.
                      Default prefix is the surface's label.

  Comments:
     - The colorized (.col) files can be loaded into SUMA (with the 'c' 
     option. By focusing on the bright spots, you can find trouble spots
     which would otherwise be very difficult to locate.
     - You should also pay attention to the messages output when the 
     surfaces are being loaded, particularly to edges (segments that 
     join 2 nodes) are shared by more than 2 triangles. For a proper
     closed surface, every segment should be shared by 2 triangles. 
     For cut surfaces, segments belonging to 1 triangle only form
     the edge of that surface.
     - There are no utilities within SUMA to correct these defects.
     It is best to fix these problems with the surface creation
     software you are using.
     - Some warnings may be redundant. That should not hurt you.
   [-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