MeshFromDiscreteFiberODF
========================

.. code-block:: none

  
  USAGE: 
  
     MeshFromDiscreteFiberODF  [--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>>] [--tau <double>]
                               [--colorscheme <DIRECTION|MAGNITUDE>]
                               [--nostretch] [--removenegative] [--basisType
                               <TENSOR|CYLINDER>] [--basicshape <TETRAHEDRON
                               |OCTAHEDRON|ICOSAHEDRON>] [--tessorder <int>]
                               [--scale <double>] [--slice
                               <std::vector<int>>] [--box <std::vector<int>>]
                               [--flip <std::vector<int>>] [--pow <double>]
                               [--iso] [--tensorISO <double>] [--tensor
                               <std::vector<double>>] [--odfOrder <int>]
                               [--outputType <DWI|EAP|ODF>] [--radius
                               <double>] [--normalize <NONE|MIN_MAX|UNIT_MAX
                               |UNIT_INTEGRAL>] [--orientations
                               <std::string>] [--mask <std::string>] [-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)
  
     --tau <double>
       Tau value. The default is calculated based on 4*pi*pi*tau=1. (value:
       0.0253303)
  
     --colorscheme <DIRECTION|MAGNITUDE>
       Color scheme. (value: DIRECTION)
  
     --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)
  
     --removenegative
       Remove negative values if set. (value: 0)
  
     --basisType <TENSOR|CYLINDER>
       Type of basis. (value: TENSOR)
  
     --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)
  
     --iso
       If set, use isotropic component. (value: 0)
  
     --tensorISO <double>
       Isotropic component for tensor. If it is negative, do not use
       isotropic component. (value: -1)
  
     --tensor <std::vector<double>>
       Three eigenvalues for tensor basis. If two are given, then the last
       two eigenvalues are the same. (value: 0.0017,0.0002,0.0002)
  
     --odfOrder <int>
       Order for the ODF output. (value: 2)
  
     --outputType <DWI|EAP|ODF>
       Type of output. (value: DWI)
  
     --radius <double>
       Radius for DWI/EAP profile.         It is b value if outputType==DWI. 
       It is r value if outputType==EAP or outputType==ODF. (value: -1)
  
     --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)
  
     --orientations <std::string>
       text file which contains orientations. If it is not set, the output is
       SH coefficients. If set, the output is EAP/DWI samples
  
     --mask <std::string>
       Mask file.
  
     -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.
  
  
     Description: Create a mesh (a spherical profile of DWI/EAP/ODF) from
     discrete fiber ODF for visualization.
  
     Examples: 
  
     MeshFromDiscreteFiberODF dwi_bw.spr -o dwi_odf_vis.vtk --tessorder 4
     --basisType TENSOR --tensor 0.0017,0.0002  --scale 1.5 --colorscheme
     MAGNITUDE --outputType ODF --tensorISO 0.7e-3  --iso 
  
     MeshFromDiscreteFiberODF dwi_bw.spr --tessorder 4 --basisType TENSOR
     --tensor 0.0017,0.0002  --scale 1.5 --colorscheme MAGNITUDE --outputType
     ODF --tensorISO 0.7e-3  --iso
  
     Author(s): Jian Cheng (jian.cheng.1983@gmail.com)
  
     Acknowledgements: Thank you everyone.