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.
 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.
       stl: STL format, ascii or binary.
            This format of no use for much of the surface-based
            analyses. Objects are defined as a soup of triangles
            with no information about which edges they share. STL is only
            useful for taking surface models to some 3D printing
            software.
       mni: MNI .obj format, ascii only.
            Only vertex, triangulation, and node normals 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.
       obj: OBJ file format for triangular meshes only. The following
            primitives are preserved: v (vertices), f (faces, triangles
            only), and p (points)
 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.

 You can also specify multiple surfaces after -i option. This makes
 it possible to use wildcards on the command line for reading in a bunch
 of surfaces at once.

     -onestate: Make all -i_* surfaces have the same state, i.e.
                they all appear at the same time in the viewer.
                By default, each -i_* surface has its own state.
                For -onestate to take effect, it must precede all -i
                options with on the command line.
     -anatomical: Label all -i surfaces as anatomically correct.
                Again, this option should precede the -i_* options.

 More variants for option -i:
-----------------------------
 You can also load standard-mesh spheres that are formed in memory
 with the following notation
     -i ldNUM:  Where NUM is the parameter controlling
                the mesh density exactly as the parameter -ld linDepth
                does in CreateIcosahedron. For example:
                    suma -i ld60
                create on the fly a surface that is identical to the
                one produced by: CreateIcosahedron -ld 60 -tosphere
     -i rdNUM: Same as -i ldNUM but with NUM specifying the equivalent
               of parameter -rd recDepth in CreateIcosahedron.

 To keep the option confusing enough, you can also use -i to load
 template surfaces. For example:
           suma -i lh:MNI_N27:ld60:smoothwm
 will load the left hemisphere smoothwm surface for template MNI_N27
 at standard mesh density ld60.
 The string following -i is formatted thusly:
     HEMI:TEMPLATE:DENSITY:SURF where:
     HEMI specifies a hemisphere. Choose from 'l', 'r', 'lh' or 'rh'.
          You must specify a hemisphere with option -i because it is
          supposed to load one surface at a time.
          You can load multiple surfaces with -spec which also supports
          these features.
     TEMPLATE: Specify the template name. For now, choose from MNI_N27 if
               you want to use the FreeSurfer reconstructed surfaces from
               the MNI_N27 volume, or TT_N27
               Those templates must be installed under this directory:
                 /home/afniHQ/.afni/data/
               If you have no surface templates there, download
                 https://afni.nimh.nih.gov/pub/dist/tgz/suma_MNI_N27.tgz
               and/or
                 https://afni.nimh.nih.gov/pub/dist/tgz/suma_TT_N27.tgz
               and/or
                 https://afni.nimh.nih.gov/pub/dist/tgz/suma_MNI152_2009.tgz
               and untar them under directory /home/afniHQ/.afni/data/
     DENSITY: Use if you want to load standard-mesh versions of the template
              surfaces. Note that only ld20, ld60, ld120, and ld141 are in
              the current distributed templates. You can create other
              densities if you wish with MapIcosahedron, but follow the
              same naming convention to enable SUMA to find them.
     SURF: Which surface do you want. The string matching is partial, as long
           as the match is unique.
           So for example something like: suma -i l:MNI_N27:ld60:smooth
           is more than enough to get you the ld60 MNI_N27 left hemisphere
           smoothwm surface.
     The order in which you specify HEMI, TEMPLATE, DENSITY, and SURF, does
     not matter.
     For template surfaces, the -sv option is provided automatically, so you
     can have SUMA talking to AFNI with something like:
             suma -i l:MNI_N27:ld60:smooth &
             afni -niml /home/afniHQ/.afni/data/suma_MNI_N27

 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
           MNI: MNI obj ascii 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.
     As with option -i, you can load template
     spec files with symbolic notation trickery as in:
                    suma -spec MNI_N27
     which will load the all the surfaces from template MNI_N27
     at the original FreeSurfer mesh density.
  The string following -spec is formatted in the following manner:
     HEMI:TEMPLATE:DENSITY where:
     HEMI specifies a hemisphere. Choose from 'l', 'r', 'lh', 'rh', 'lr', or
          'both' which is the default if you do not specify a hemisphere.
     TEMPLATE: Specify the template name. For now, choose from MNI_N27 if
               you want surfaces from the MNI_N27 volume, or TT_N27
               for the Talairach version.
               Those templates must be installed under this directory:
                 /home/afniHQ/.afni/data/
               If you have no surface templates there, download one of:
                 https://afni.nimh.nih.gov/pub/dist/tgz/suma_MNI_N27.tgz
                 https://afni.nimh.nih.gov/pub/dist/tgz/suma_TT_N27.tgz
                 https://afni.nimh.nih.gov/pub/dist/tgz/suma_MNI152_2009.tgz
               and untar them under directory /home/afniHQ/.afni/data/
     DENSITY: Use if you want to load standard-mesh versions of the template
              surfaces. Note that only ld20, ld60, ld120, and ld141 are in
              the current distributed templates. You can create other
              densities if you wish with MapIcosahedron, but follow the
              same naming convention to enable SUMA to find them.
              This parameter is optional.
     The order in which you specify HEMI, TEMPLATE, and DENSITY, does
     not matter.
     For template surfaces, the -sv option is provided automatically, so you
     can have SUMA talking to AFNI with something like:
             suma -spec MNI_N27:ld60 &
             afni -niml /home/afniHQ/.afni/data/suma_MNI_N27

 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.

   [-novolreg]: Ignore any Rotate, Volreg, Tagalign,
                or WarpDrive transformations present in
                the Surface Volume.
   [-noxform]: Same as -novolreg
   [-setenv "'ENVname=ENVvalue'"]: Set environment variable ENVname
                to be ENVvalue. Quotes are necessary.
             Example: suma -setenv "'SUMA_BackgroundColor = 1 0 1'"
                See also options -update_env, -environment, etc
                in the output of 'suma -help'
  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.


Global Options (available to all AFNI/SUMA programs)
  -h: Mini help, at time, same as -help in many cases.
  -help: The entire help output
  -HELP: Extreme help, same as -help in majority of cases.
  -h_view: Open help in text editor. AFNI will try to find a GUI editor
  -hview : on your machine. You can control which it should use by
           setting environment variable AFNI_GUI_EDITOR.
  -h_web: Open help in web browser. AFNI will try to find a browser.
  -hweb : on your machine. You can control which it should use by
          setting environment variable AFNI_GUI_EDITOR.
  -h_find WORD: Look for lines in this programs's -help output that match
                (approximately) WORD.
  -h_raw: Help string unedited
  -h_spx: Help string in sphinx loveliness, but do not try to autoformat
  -h_aspx: Help string in sphinx with autoformatting of options, etc.
  -all_opts: Try to identify all options for the program from the
             output of its -help option. Some options might be missed
             and others misidentified. Use this output for hints only.



Compile Date:
   Oct 31 2024