DWISingleVoxelSimulatorΒΆ

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.). (default: 0)

   --xml
     Produce xml description of command line arguments (default: 0)

   --echo
     Echo the command line arguments (default: 0)

   --debug
     debug (default: 0)

   --elecnumber <int>
     Number of stored gradient by electrostatic energy minimization.
     (default: -1)

   --tessorder <int>
     Tessellation order for UNIFORM random type. (default: -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. (default:
     FIXED)

   --outputdwitype <4D|4DALL|EACHSHELL>
     Output DWI type. (default: 4DALL)

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

   --tau <float>
     Used for calculating q values from b values. The default value is set
     so that 4*pi^2*tau=1. (default: 0.0253303)

   --snr <float>
     Signal-to-Noise Ratio. Conflicts with noisesigma. (default: 0)

   --noisesigma <float>
     Noise level. Conflicts with snr. (default: 0)

   --b0scale <float>
     The value of b0 image. (default: 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. (default: 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. (default: 1,1,1)

   --modeltype <TENSOR_CARTESIAN|TENSOR_SPHERICAL|CYLINDER_SPHERICAL>
     Type of input diffusion parameters. (default: 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.