DWISingleVoxelSimulator
=======================

.. code-block:: none

  
  USAGE: 
  
     DWISingleVoxelSimulator  [--returnparameterfile <std::string>]
                              [--processinformationaddress <std::string>]
                              [--xml] [--echo] [--debug] [--elecnumber <int>]
                              [--tessorder <int>] [--randomtype <FIXED
                              |UNIFORM>] [--outputdwitype <4D|4DALL
                              |EACHSHELL>] [--peaks <int>] [--tau <float>]
                              [--snr <float>] [--noisesigma <float>]
                              [--b0scale <float>] [--rvalues
                              <std::vector<double>>] [--rfile <std::string>]
                              [--rorientations <std::string>] [--bvalues
                              <std::vector<double>>] [--bfile <std::string>]
                              [--qorientations <std::string>] [--outb0
                              <std::string>] [--peaktype <XYZV|XYZ|NXYZV
                              |NXYZ>] [--outmsd <std::string>] [--outrto
                              <std::string>] [--outpeak <std::string>]
                              [--outeap <std::string>] [--outodf
                              <std::string>] [--outdwi <std::string>] [--size
                              <std::vector<int>>] [--modeltype
                              <TENSOR_CARTESIAN|TENSOR_SPHERICAL
                              |CYLINDER_SPHERICAL>] [--params
                              <std::vector<double>>] [--] [--version] [-h]
  
  
  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)
  
     --elecnumber <int>
       Number of stored gradient by electrostatic energy minimization.
       (value: -1)
  
     --tessorder <int>
       Tessellation order for UNIFORM random type. (value: -1)
  
     --randomtype <FIXED|UNIFORM>
       Random Type to rotate the given diffusion parameter in voxels. If
       UNIFORM is used, then the uniform orientation is randomly generated or
       from --tessorder or --elecnumber if one of them is set. (value:
       FIXED)
  
     --outputdwitype <4D|4DALL|EACHSHELL>
       Output DWI type. (value: 4DALL)
  
     --peaks <int>
       Maximal number of peaks for output peak file. (value: 4)
  
     --tau <float>
       Used for calculating q values from b values. The default value is set
       so that 4*pi^2*tau=1. (value: 0.0253303)
  
     --snr <float>
       Signal-to-Noise Ratio. Conflicts with noisesigma. (value: 0)
  
     --noisesigma <float>
       Noise level. Conflicts with snr. (value: 0)
  
     --b0scale <float>
       The value of b0 image. (value: 1)
  
     --rvalues <std::vector<double>>
       R values for different shells. Each shell uses the same orientations
       specified with rgradients. Conflicts with rfile.
  
     --rfile <std::string>
       Text file that contains the R values. The number of entries should be
       consistent with the orientations specified with rgradients.
  
     --rorientations <std::string>
       Text file that contains the orientations for sampling in the R-space.
  
     --bvalues <std::vector<double>>
       B values for different shells. Each shell uses the same orientations
       specified with qgradients. Conflicts with bfile.
  
     --bfile <std::string>
       Text file that contains the B values. The number of entries should be
       consistent with the orientations specified with qgradient. Conflicts
       with bvalues.
  
     --qorientations <std::string>
       Text file that contains the gradient orientations of the data.
  
     --outb0 <std::string>
       Output B0 image.
  
     --peaktype <XYZV|XYZ|NXYZV|NXYZ>
       Peak Type. XYZV: peak direction vector (x,y,z) + peak magnitude v;
       XYZ: peak direction vector; NXYZV: number of peaks + peak direction
       vectors + peak magnitudes; NXYZ: number of peaks + peak direction
       vectors. (value: XYZV)
  
     --outmsd <std::string>
       Scalar image that will contain the mean squared displacement (MSD)
       probability map.
  
     --outrto <std::string>
       Scalar image that will contain the return-to-origin (RTO) probability
       map.
  
     --outpeak <std::string>
       Vector image that will contain the ground truch of peaks.
  
     --outeap <std::string>
       Vector image that will contain the EAP field.
  
     --outodf <std::string>
       Vector image that will contain the ODF field.
  
     --outdwi <std::string>
       Vector image that will contain the DWI field.
  
     --size <std::vector<int>>
       Image size. (value: 1,1,1)
  
     --modeltype <TENSOR_CARTESIAN|TENSOR_SPHERICAL|CYLINDER_SPHERICAL>
       Type of input diffusion parameters. (value: TENSOR_SPHERICAL)
  
     --params <std::vector<double>>
       diffusion parameters.
  
     --,  --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.
  
  
     Description: Simulate DWI data with fixed single voxel
     configuration.
  
     Author(s): Jian Cheng (jian.cheng.1983@gmail.com)
  
     Acknowledgements: Thank you everyone.