TubeTK/Documentation/EnhanceCoherenceUsingDiffusion

  Description: Performs coherence enhancing anisotropic diffusion: smooths
  flow-like structures (ex. vessels/tubes). Strong smoothing is performed
  in the direction of least intensity contrast (i.e. parallel to the
  tube). Implemented as described in Mendrik et al., Noise reduction in
  computed tomography scans using 3-D anisotropic diffusion with
  continuous switch, IEEE Transactions on Medical Imaging, 28(10), pp.
  1585-1594, 2009.

USAGE:

  ./EnhanceCoherenceUsingDiffusion  [--returnparameterfile <std::string>]
                                    [--processinformationaddress
                                    <std::string>] [--xml] [--echo] [-n
                                    <int>] [-t <double>] [-a <double>] [-c
                                    <double>] [-s <double>] [--]
                                    [--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.). (default: 0)

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

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

  -n <int>,  --numIterations <int>
    Number of iterations used in optimization. (default: 1)

  -t <double>,  --timeStep <double>
    Time step used in optimization. (default: 0.11)

  -a <double>,  --alpha <double>
    Regularization parameter to ensure that the diffusion tensor matrix is
    positive definite and to prevent division by zero. Should be set to
    something very small. (default: 0.001)

  -c <double>,  --CEDContrast <double>
    Ratio between the second and third eigenvalues that indicates a
    tube-like structure. If set too low, small spherical structures will
    not be preserved. If set too high, tubular structures will not be
    filtered. (default: 15)

  -s <double>,  --scale <double>
    Scale at which first derivatives are calculated when determining the
    structure tensor and gradient magnitude. If set too low, filter will
    be overly sensitive to noise. If set too high, small structures will
    not be well preserved. (default: 1)

  --,  --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 volume.

  <std::string>
    (required)  Output volume.

  Author(s): Danielle F. Pace, Andinet Enquobahrie, Hua Yang, Stephen R.
  Aylward (Kitware)

  Acknowledgements: This work is part of the TubeTK project at Kitware.