DWISimulator

USAGE:

   DWISimulator  [--returnparameterfile <std::string>]
                 [--processinformationaddress <std::string>] [--xml]
                 [--echo] [--debug] [--outputdwitype <4D|4DALL|EACHSHELL>]
                 [--tau <float>] [--snr <float>] [--noisesigma <float>]
                 [--bgdiffusionparams <std::vector<double>>]
                 [--cylinderparams <std::vector<double>>] [--rvalues
                 <std::vector<double>>] [--rfile <std::string>]
                 [--rorientations <std::string>] [--bvalues
                 <std::vector<double>>] [--bfile <std::string>]
                 [--qorientations <std::string>] [--outb0 <std::string>]
                 [--peaks <int>] [--peaktype <XYZV|XYZ|NXYZV|NXYZ>]
                 [--outmsd <std::string>] [--outrto <std::string>]
                 [--outpeak <std::string>] [--outeap <std::string>]
                 [--outodf <std::string>] [--outdwi <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)

   --outputdwitype <4D|4DALL|EACHSHELL>
     Output DWI type. 4D: only 4D dwi image. 4DALL: one 4D dwi image (with
     all b values), gradient file and b values in a txt file. EACHSHELL:
     several 4D DWI images (with different b values), gradient file and b
     values in a txt file (value: 4DALL)

   --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 (overrides parameter file value). Conflicts with
     --noisesigma. (value: 0)

   --noisesigma <float>
     Noise level (overrides parameter file value). Conflicts with --snr.
     (value: 0)

   --bgdiffusionparams <std::vector<double>>
     Background diffusion parameters; override parameters in parameter file

   --cylinderparams <std::vector<double>>
     Parameters in clinder model. (Length,radius,diffusivity) (value: 5.0
     ,0.005,2.02e-3)

   --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.

   --peaks <int>
     Maximal number of peaks for output peak file. (value: 4)

   --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.

   --,  --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 the diffusion parameters.


   Description: Simulate DWI data.

   Examples:

   DWISimulator dwi_config.txt --outdwi dwi.nii.gz --outodf odfTrue.nii.gz
   --outeap eapTrue_r0.015.nii.gz  --qorientations Elec060.txt --bvalues
   1000,2000,3000 --rorientations directions_t4.txt --rvalues 0.015
   --noisesigma 0.0 --outb0 dwi_diagonal_b0.nii.gz --outputdwitype
   EACHSHELL

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

   Acknowledgements: Thank you everyone.