SphericalPolarFourierImaging
============================

.. code-block:: none

  
  USAGE: 
  
     SphericalPolarFourierImaging  [--returnparameterfile <std::string>]
                                   [--processinformationaddress
                                   <std::string>] [--xml] [--echo] [-v <int>]
                                   [-p] [--nt <int>] [--md0 <double>] [--tau
                                   <double>] [--mask <std::string>]
                                   [--lambdaL1 <double>] [--minChange
                                   <double>] [--maxIter <int>] [--solver
                                   <FISTA_LS|SPAMS>] [--estimation <LS|L1_2
                                   |L1_DL>] [--mdImage <std::string>]
                                   [--scale <double>] [--radius <double>]
                                   [--odfOrder <int>] [--lambdaRA <double>]
                                   [--lambdaSH <double>] [--ra <int>] [--sh
                                   <int>] [--signal <std::string>] [--odf
                                   <std::string>] [--eapProfile
                                   <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)
  
     -v <int>,  --verbose <int>
       Verbose level. 0: no output log. 1: normal log. 2: log for debug log.
       3: log for large matrix or vectors. (value: 1)
  
     -p,  --progress
       show progress of processing (value: 0)
  
     --nt <int>
       Number of threads. If it not positive, then the default number for
       multiple threads is used. (value: -1)
  
     --md0 <double>
       Typical mean diffusivity (MD) value. (value: 0.0007)
  
     --tau <double>
       Tau value. The default is calculated based on 4*pi*pi*tau=1. (value:
       0.0253303)
  
     --mask <std::string>
       Mask file.
  
     --lambdaL1 <double>
       Regularization parameter for L1 optimization. (value: 1e-05)
  
     --minChange <double>
       Minimal change percentage of the cost function and variable for l1
       oprimization. (value: 0.0001)
  
     --maxIter <int>
       Maximal number of iteration in L1 FISTA. (value: 1000)
  
     --solver <FISTA_LS|SPAMS>
       Type of L1 solver. Use different L1 solver.         FISTA_LS: FISTA
       using least square initialization.         SPAMS: use spams' weighted
       lasso solver. (value: SPAMS)
  
     --estimation <LS|L1_2|L1_DL>
       Type of solver.         LS means least square.         L1_2 means
       Laplace-Beltrami weight (two regularization parameters lambdaSH and
       lambdaRA);         L1_DL only use lambdaL1, because the learned
       dictionary corresponses the regularization matrix. (value: LS)
  
     --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)
  
     --radius <double>
       Radius for EAP profile. (value: 0.015)
  
     --odfOrder <int>
       Order for the ODF output. (value: 2)
  
     --lambdaRA <double>
       Regularization lambda for radial part. (value: 0)
  
     --lambdaSH <double>
       Regularization lambda for spherical part. (value: 0)
  
     --ra <int>
       Rank for radial basis. (value: 1)
  
     --sh <int>
       Rank for SH basis. (value: 4)
  
     --signal <std::string>
       Output Image File (SPF coefficients) with basis coefficients.
  
     --odf <std::string>
       Output Image File (ODF) represented by SH basis.
  
     --eapProfile <std::string>
       Output Image File (EAP profile) represented by SH basis.
  
     --,  --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)  Text file that contains b values, gradient orientations,
       and DWI images.
  
  
     Description: Spherical Polar Fourier Imaging (SPFI): estimate SPF
     coefficients from DWI signals. 
  
     Examples: 
  
     SphericalPolarFourierImaging dwi.txt --sh 8 --ra 4 --signal
     signalSPF.nii.gz --radius 0.015 --estimation L1_DL --lambdaL1 1e-6
     --mdImage MD.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.