MeshFromSHCoefficients

USAGE:

   MeshFromSHCoefficients  [--returnparameterfile <std::string>]
                           [--processinformationaddress <std::string>]
                           [--xml] [--echo] [--debug] [-p] [--st]
                           [--nolighting] [--nonormal] [--zoom <double>]
                           [--png <std::string>] [--bg
                           <std::vector<double>>] [--angle
                           <std::vector<double>>] [--size
                           <std::vector<int>>] [--colorscheme <DIRECTION
                           |MAGNITUDE>] [--basicshape <TETRAHEDRON
                           |OCTAHEDRON|ICOSAHEDRON>] [--tessorder <int>]
                           [--scale <double>] [--slice <std::vector<int>>]
                           [--box <std::vector<int>>] [--flip
                           <std::vector<int>>] [--pow <double>]
                           [--nostretch] [--normalize <NONE|MIN_MAX
                           |UNIT_MAX|UNIT_INTEGRAL>] [--removenegative]
                           [--maxorder <int>] [--zonal] [-o <std::string>]
                           [--] [--version] [-h] <std::string>


Where:

   --returnparameterfile <std::string>
     Filename in which to write simple return parameters (int, float,
     int-vector, etc.) as opposed to bulk return parameters (image,
     geometry, transform, measurement, table).

   --processinformationaddress <std::string>
     Address of a structure to store process information (progress, abort,
     etc.). (value: 0)

   --xml
     Produce xml description of command line arguments (value: 0)

   --echo
     Echo the command line arguments (value: 0)

   --debug
     debug (value: 0)

   -p,  --progress
     show progress of processing (value: 0)

   --st
     Use single thread. (value: 0)

   --nolighting
     Set LightingOff. (value: 0)

   --nonormal
     Do not use vtkPolyDataNormals. (value: 0)

   --zoom <double>
     zoom factor. Used when visualzing the vtk file.

   --png <std::string>
     output png file. Used when visualzing the vtk file.

   --bg <std::vector<double>>
     background color for the window (value: 0,0,0)

   --angle <std::vector<double>>
     azimuth,elevation. Used when visualzing the vtk file. (value: 0.0,0.0)

   --size <std::vector<int>>
     window size. Used when visualzing the vtk file. (value: 600,600)

   --colorscheme <DIRECTION|MAGNITUDE>
     Color scheme. (value: DIRECTION)

   --basicshape <TETRAHEDRON|OCTAHEDRON|ICOSAHEDRON>
     Basic shape for subdivision. (value: ICOSAHEDRON)

   --tessorder <int>
     Tessellation order. (value: 4)

   --scale <double>
     Scale factor. (value: 1)

   --slice <std::vector<int>>
     coordinates for coronal, sagittal and transverse views. When -1 is
     used for x/y/z, then the voxel is visible in the x/y/z-axis. (value:
     -1,-1,-1)

   --box <std::vector<int>>
     only generate mesh from a given box (x0,x1,y0,y1,z0,z1). When -1 is
     used, then x0/y0/z0 will be 0, x1/y1/z1 will be the maximal number in
     the x/y/z-axis. (value: -1,-1,-1,-1,-1,-1)

   --flip <std::vector<int>>
     Flip x/y/z-axis for spherical functions. 1 means flip, 0 means
     no-flip. (value: 0,0,0)

   --pow <double>
     Power factor. (value: 1)

   --nostretch
     If it is set, the mesh in each voxel is a sphere and the values of the
     spherical function are only for coloring. (value: 0)

   --normalize <NONE|MIN_MAX|UNIT_MAX|UNIT_INTEGRAL>
     Perform normalization after removing negative values (if set); NONE:
     No normalization; MIN_MAX: Min-max normalization; UNIT_MAX: Unit
     maximum; UNIT_INTEGRATION: Unit integration. (value: NONE)

   --removenegative
     Remove negative values if set. (value: 0)

   --maxorder <int>
     Maximum order of spherical harmonic basis functions. If it is not set,
     it is calculated from the input SH image. If it is set as a smaller
     value than the order calculated from input image, then only truncated
     orders are used to generate mesh. (value: 0)

   --zonal
     SH coefficients only contains even, m=0 terms, i.e., zonal SH. It is
     used for SH coefficients of a response function. (value: 0)

   -o <std::string>,  --output <std::string>
     Output vtk file. If it is not set, visualize the vtk file. (value: "")

   --,  --ignore_rest
     Ignores the rest of the labeled arguments following this flag.

   --version
     Displays version information and exits.

   -h,  --help
     Displays usage information and exits.

   <std::string>
     (required)  Input file. It is 1) an image file with SH coefficients;
     2) or a .txt file with SH coefficients of a single spheriacl
     function.


   Description: Create a mesh from spherical harmonics coefficients for
   visualization.

   Examples:

   MeshFromSHCoefficients eap_r0.015.nii.gz -o eap_r0.015_vis.vtk
   --tessorder 4 --scale 1e-5

   MeshFromSHCoefficients eap_r0.015.nii.gz --tessorder 4 --scale 1e-5

   MeshFromSHCoefficients eap_r0.015.nii.gz --tessorder 4 --scale 1e-5
   --png out.png

   MeshFromSHCoefficients odf.nii.gz -o odf_vis.vtk --tessorder 4 --scale
   1.5

   MeshFromSHCoefficients odf.nii.gz -o odf_vis.vtk --tessorder 4 --scale
   1.5 --slice -1,-1,25

   MeshFromSHCoefficients odf.nii.gz -o odf_vis.vtk --tessorder 4 --scale
   1.5 --box 20,40,20,40,25,25

   MeshFromSHCoefficients sh.txt --nonormal --colorscheme MAGNITUDE

   MeshFromSHCoefficients sh.txt --nonormal --colorscheme MAGNITUDE
   --nostretch

   MeshFromSHCoefficients sh_zonal.txt --zonal --nonormal --colorscheme
   MAGNITUDE

   Author(s): Pew-Thian Yap (ptyap@med.unc.edu), Jian Cheng
   (jian.cheng.1983@gmail.com)

   Acknowledgements: Thank you everyone.