TubeTK/Documentation/RegisterImages

  Description: Provides rigid, affine, and BSpline registration methods
  via a simple GUI

USAGE:

  ./RegisterImages  [--returnparameterfile <std::string>]
                    [--processinformationaddress <std::string>] [--xml]
                    [--echo] [--controlPointSpacing <int>]
                    [--bsplineSamplingRatio <float>]
                    [--bsplineMaxIterations <int>] [--affineSamplingRatio
                    <float>] [--affineMaxIterations <int>]
                    [--rigidSamplingRatio <float>] [--rigidMaxIterations
                    <int>] [--movingLandmarks
                    <std::vector<std::vector<float> >>] ... 
                    [--fixedLandmarks <std::vector<std::vector<float> >>]
                    ...  [--interpolation <NearestNeighbor|Linear
                    |BSpline>] [--minimizeMemory] [--numberOfThreads
                    <int>] [--randomNumberSeed <int>] [--fixedImageMask
                    <std::string>] [--sampleFromOverlap] [--verbosityLevel
                    <Silent|Standard|Verbose>] [--expectedSkew <float>]
                    [--expectedScale <float>] [--expectedRotation <float>]
                    [--expectedOffset <float>] [--metric <MattesMI
                    |NormCorr|MeanSqrd>] [--registration <None|Initial
                    |Rigid|Affine|BSpline|PipelineRigid|PipelineAffine
                    |PipelineBSpline>] [--initialization <None|Landmarks
                    |ImageCenters|CentersOfMass|SecondMoments>]
                    [--saveDisplacementField <std::string>]
                    [--saveTransform <std::string>] [--loadTransform
                    <std::string>] [--resampledImage <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)

  --controlPointSpacing <int>
    Number of pixels between control points (default: 40)

  --bsplineSamplingRatio <float>
    Portion of the image to use in computing the metric during BSpline
    registration (default: 0.1)

  --bsplineMaxIterations <int>
    Maximum number of bspline optimization iterations (default: 20)

  --affineSamplingRatio <float>
    Portion of the image to use in computing the metric during affine
    registration (default: 0.02)

  --affineMaxIterations <int>
    Maximum number of affine optimization iterations (default: 50)

  --rigidSamplingRatio <float>
    Portion of the image to use in computing the metric during rigid
    registration (default: 0.01)

  --rigidMaxIterations <int>
    Maximum number of rigid optimization iterations (default: 100)

  --movingLandmarks <std::vector<std::vector<float> >>  (accepted multiple
     times)
    Ordered list of landmarks in the moving image

  --fixedLandmarks <std::vector<std::vector<float> >>  (accepted multiple
     times)
    Ordered list of landmarks in the fixed image

  --interpolation <NearestNeighbor|Linear|BSpline>
    Method for interpolation within the optimization process (default:
    Linear)

  --minimizeMemory
    Reduce the amount of memory required at the cost of increased
    computation time (default: 0)

  --numberOfThreads <int>
    Number of CPU threads to use (default: 0)

  --randomNumberSeed <int>
    Seed to generate a consistent random number sequence (default: 0)

  --fixedImageMask <std::string>
    Image which defines a mask for the fixed image

  --sampleFromOverlap
    Limit metric evaluation to the fixed image region overlapped by the
    moving image (default: 0)

  --verbosityLevel <Silent|Standard|Verbose>
    Level of detail of reporting progress (default: Standard)

  --expectedSkew <float>
    Expected misalignment after initialization (default: 0.01)

  --expectedScale <float>
    Expected misalignment after initialization (default: 0.05)

  --expectedRotation <float>
    Expected misalignment after initialization (default: 0.1)

  --expectedOffset <float>
    Expected misalignment after initialization (default: 10)

  --metric <MattesMI|NormCorr|MeanSqrd>
    Method to quantify image match (default: MattesMI)

  --registration <None|Initial|Rigid|Affine|BSpline|PipelineRigid
     |PipelineAffine|PipelineBSpline>
    Method for the registration process (default: PipelineAffine)

  --initialization <None|Landmarks|ImageCenters|CentersOfMass
     |SecondMoments>
    Method to prime the registration process (default: CentersOfMass)

  --saveDisplacementField <std::string>
    Save displacement field result from registration

  --saveTransform <std::string>
    Save the transform that results from registration

  --loadTransform <std::string>
    Load a transform that is immediately applied to the moving image

  --resampledImage <std::string>
    Registration results

  --,  --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)  Image which defines the space into which the moving image
    is registered

  <std::string>
    (required)  The transform goes from the fixed image's space into the
    moving image's space

  Author(s): Stephen R Aylward (Kitware), Casey B Goodlett
  (Kitware)

  Acknowledgements: This work is part of the National Alliance for Medical
  Image Computing (NAMIC), funded by the National Institutes of Health
  through the NIH Roadmap for Medical Research, Grant U54 EB005149.