Modules:EM-Segmenter-Documentation:CommandLineInterface

USAGE:

  ./EMSegmentCommandLine  [--processinformationaddress <std::string>]
                          [--xml] [--echo] [--disableCompression]
                          [--resultMRMLSceneFileName <std::string>]
                          [--generateEmptyMRMLSceneAndQuit <std::string>]
                          [--dontWriteResults]
                          [--resultStandardVolumeFileName <std::string>]
                          [--verbose] [--dontUpdateIntermediateData]
                          [--disableMultithreading]
                          [--parametersMRMLNodeName <std::string>]
                          [--intermediateResultsDirectory <std::string>]
                          [--atlasVolumeFileNames
                          <std::vector<std::string>>] ... 
                          [--targetVolumeFileNames
                          <std::vector<std::string>>] ... 
                          [--resultVolumeFileName <std::string>]
                          [--mrmlSceneFileName <std::string>] [--]
                          [--version] [-h]

Where:

  --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)

  --disableCompression
    Don't use compression when writing result image to disk. (default: 0)

  --resultMRMLSceneFileName <std::string>
    Write out the MRML scene after command line substitutions have been
    made.

  --generateEmptyMRMLSceneAndQuit <std::string>
    Used for testing.  Only write a scene with default mrml parameters.

  --dontWriteResults
    Used for testing.  Don't actually write the resulting labelmap to
    disk. (default: 0)

  --resultStandardVolumeFileName <std::string>
    Used for testing.  Compare segmentation results to this image and
    return EXIT_FAILURE if they do not match.

  --verbose
    Enable verbose output. (default: 0)

  --dontUpdateIntermediateData
    Disable update of intermediate results. (default: 0)

  --disableMultithreading
    Disable multithreading. (default: 0)

  --parametersMRMLNodeName <std::string>
    The name of the EMSegment parameters node within the active MRML
    scene.  Leave blank for default.

  --intermediateResultsDirectory <std::string>
    Directory where EMSegmenter will write intermediate data (e.g.,
    aligned atlas data).

  --atlasVolumeFileNames <std::vector<std::string>>  (accepted multiple
     times)
    File names of atlas (spatial) probability maps.  The number of atlas
    volumes must match the number specified in the parameter set.  The
    ordering must match the ordering defined in the mrml parameters file.

  --targetVolumeFileNames <std::vector<std::string>>  (accepted multiple
     times)
    File names of target volumes (to be segmented).  The number of target
    images must be equal to the number of target images specified in the
    parameter set, and these images must be spatially aligned.

  --resultVolumeFileName <std::string>
    The file name that the segmentation result volume will be written to.

  --mrmlSceneFileName <std::string>
    Active MRML scene that contains EMSegment algorithm 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: EMSegment command-line module description and
  help.

  Author(s): Brad Davis

  Acknowledgements: Many people and organizations have contributed to the
  funding, design, and development of the EMSegment algorithm and its
  various implementations.