TubeTK/Documentation/SegmentTubes

  Description: Extracts a 1D scaled ridge and estimate its radius in an ND
  image.

USAGE:

  ./SegmentTubes  [--returnparameterfile <std::string>]
                  [--processinformationaddress <std::string>] [--xml]
                  [--echo] [-o <std::string>] [-P <std::string>] [-b
                  <double>] [-T <int>] [-S <std::string>] [-M
                  <std::string>] [-p <std::vector<std::vector<float> >>]
                  ...  [-i <std::vector<std::vector<float> >>] ...  [-s
                  <double>] [-f <std::string>] [--] [--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)

  -o <std::string>,  -- <std::string>
    Output binary mask of extracted tubes

  -P <std::string>,  --parametersFile <std::string>
    Parameters for ridge and radius extraction

  -b <double>,  --border <double>
    Distance from edge (in voxels) to ignore (default: 5)

  -T <int>,  --seedMaskStride <int>
    Only use 1/stride seed points (default: 4)

  -S <std::string>,  --scaleMask <std::string>
    Intensity is initial extraction scale for that point

  -M <std::string>,  --seedMask <std::string>
    Image mask where non-zero values are used as seeds.

  -p <std::vector<std::vector<float> >>,  --seedP
     <std::vector<std::vector<float> >>  (accepted multiple times)
    Phisycal coordinate seed for ridge extraction

  -i <std::vector<std::vector<float> >>,  --seedI
     <std::vector<std::vector<float> >>  (accepted multiple times)
    Continuous index for starting ridge extraction

  -s <double>,  --scale <double>
    Scale used for ridge measures (default: 2)

  -f <std::string>,  --seedList <std::string>
    List seed points stored in a file

  --,  --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 tube file

  Author(s): Stephen R. Aylward (Kitware)

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