TubeTK/Documentation/AtlasBuilderUsingIntensity

Description: Computes an atlas from a set of subject-specific files.

USAGE:

  ./AtlasBuilderUsingIntensity  [--returnparameterfile <std::string>]
                                [--processinformationaddress
                                <std::string>] [--xml] [--echo]
                                [--outputSpacing <std::vector<int>>]
                                [--outputSize <std::vector<double>>]
                                [--lowerThreshold <int>]
                                [--useStdDeviation]
                                [--doImageOriginAdjustment]
                                [--doImageSizeAdjustment]
                                [--outputCountImage <std::string>] [--]
                                [--version] [-h] <std::string>
                                <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)

  --outputSpacing <std::vector<int>>
    Output image spacing. Default is the initial image spacing.

  --outputSize <std::vector<double>>
    Output image size (X,Y,Z). Cannot use with --doImageSizeAdjustment.

  --lowerThreshold <int>
    Minimum number of contributing images for pixel to be counted in
    output. (default: 4)

  --useStdDeviation
    Is the sigma image standard deviation? (default: 0)

  --doImageOriginAdjustment
    Adjust the mean origin to the input images. (default: 0)

  --doImageSizeAdjustment
    Adjust the mean size to the input images. (default: 0)

  --outputCountImage <std::string>
    Filename to save the count image.

  --,  --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)  Object document with Euclidean distance map information.

  <std::string>
    (required)  Output (mean) atlas computed from subject-specific files.

  <std::string>
    (required)  Output (variance) atlas computed from subject-specific
    files.

  Author(s): Stephen R. Aylward, Roland Kwitt (Kitware)

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