SPFToScalarMap
==============

.. code-block:: none

  
  USAGE: 
  
     SPFToScalarMap  [--returnparameterfile <std::string>]
                     [--processinformationaddress <std::string>] [--xml]
                     [--echo] [--debug] [-p] [--md0 <double>] [--tau
                     <double>] [--nt <int>] [--mask <std::string>] [--mapType
                     <RTO|MSD|PFA>] [--mdImage <std::string>] [--scale
                     <double>] [--ra <int>] [--sh <int>] [--] [--version]
                     [-h] <std::string> <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)
  
     --md0 <double>
       Typical MD value. (value: 0.0007)
  
     --tau <double>
       Tau value. The default is calculated based on 4*pi*pi*tau=1. (value:
       0.0253303)
  
     --nt <int>
       Number of threads. If it not positive, then the default number for
       multiple threads is used. (value: -1)
  
     --mask <std::string>
       Mask file.
  
     --mapType <RTO|MSD|PFA>
       Type of scalar maps. (value: RTO)
  
     --mdImage <std::string>
       Mean diffusivity Image for adaptive scale.
  
     --scale <double>
       Scale for SPF basis. If it is negative, the default value based on
       typical MD is used. (value: -1)
  
     --ra <int>
       Rank for radial basis. (value: 1)
  
     --sh <int>
       Rank for SH basis. (value: 4)
  
     --,  --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 Image File represented by SPF basis.
  
     <std::string>
       (required)  Output Image File (scalar map).
  
  
     Description: Estimate scalar maps using SPFI. 
  
     Examples: 
  
     SPFToScalarMap signalSPF.nii.gz rto.nii.gz --mapType RTO  --sh 8 --ra 4
     --mdImage D_sh4_ra1.nii.gz 
  
     SPFToScalarMap signalSPF.nii.gz msd.nii.gz --mapType MSD  --sh 8 --ra 4
     --mdImage D_sh4_ra1.nii.gz 
  
     SPFToScalarMap signalSPF.nii.gz pfa.nii.gz --mapType PFA  --sh 8 --ra 4
     --mdImage D_sh4_ra1.nii.gz 
  
     Reference: 
  
     Jian Cheng, Aurobrata Ghosh, Rachid Deriche, Tianzi Jiang, 'Model-Free,
     Regularized, Fast, and Robust Analytical Orientation Distribution
     Function Estimation', Medical Image Computing and Computer-Assisted
     Intervention (MICCAI'10), vol. 6361, pp. 648–656, sep, 2010.  
  
     Jian Cheng, Aurobrata Ghosh, Tianzi Jiang, Rachid Deriche, 'Model-free
     and Analytical EAP Reconstruction via Spherical Polar Fourier Diffusion
     MRI', Medical Image Computing and Computer-Assisted Intervention
     (MICCAI'10), vol. 6361, pp. 590–597, sep, 2010.
  
     Author(s): Jian Cheng (jian.cheng.1983@gmail.com)
  
     Acknowledgements: Thank you everyone.