View source for TubeTK/Documentation/RegisterUsingSlidingGeometries

   Description: Performs registration between images depicting sliding
   organs, using an anisotropic diffusive regularization.

USAGE: 

   ./RegisterUsingSlidingGeometries  [--returnparameterfile <std::string>]
                                     [--processinformationaddress
                                     <std::string>] [--xml] [--echo] [-c
                                     <RAS|LPS>] [-u <SlidingOrgan
                                     |SparseSlidingOrgan>] [-a]
                                     [--doNotComputeIntensityDistanceTerm]
                                     [-r] [-g <double>] [-l <double>] [-z
                                     <std::string>] [-x <std::string>] [-v
                                     <std::string>] [-o <std::string>] [-d
                                     <std::string>]
                                     [--stoppingCriterionMask
                                     <std::string>] [--backgroundIntensity
                                     <double>] [-q <std::string>] [-t
                                     <std::string>] [-e <std::string>] [-w
                                     <std::string>] [-n <std::string>] [-p
                                     <std::string>] [-b <std::string>] [-m
                                     <double>] [--maximumTotalEnergyChange
                                     <double>] [--stoppingCriterionPeriod
                                     <int>] [-k <std::vector<double>>] [-s
                                     <double>] [-i <std::vector<int>>] [--]
                                     [--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)

   -c <RAS|LPS>,  --worldCoordinateSystem <RAS|LPS>
     The world coordinate system. RAS if the images and model are aligned
     when visualized in 3D Slicer, LPS if the images and model are aligned
     when visualized in Paraview. (default: RAS)

   -u <SlidingOrgan|SparseSlidingOrgan>,  --anisotropicRegistrationType
      <SlidingOrgan|SparseSlidingOrgan>
     The type of the anisotropic registration. Each voxel has one normal in
     the 'sliding organ' type, and three normals in the 'sparse sliding
     organ' type. 'sparse sliding organ' is under development and not
     recommended. (default: SlidingOrgan)

   -a,  --doNotUseAnisotropicRegularization
     Whether or not to use the anisotropic diffusive regularization (if
     true, uses the diffusive regularization (i.e. Gaussian smoothing).
     (default: 0)

   --doNotComputeIntensityDistanceTerm
     Whether or not to compute the intensity distance term. (default: 0)

   -r,  --doNotPerformRegularization
     Whether or not to perform motion field regularization. (default: 0)

   -g <double>,  --gamma <double>
     Controls the Dirac-shaped function used to calculate the weight value
     as a function of the distance to the closest organ border point. Must
     be positive to use a Dirac-shaped function. If gamma = -1, then an
     exponential decay using lambda will be used instead (default
     behavior). (default: -1)

   -l <double>,  --lambda <double>
     Controls the function used to calculate the weight value as a function
     of the distance to the closest organ border point. If gamma = -1, then
     the function is exponential decay. Otherwise, the function is a
     Dirac-shaped function. Must be positive. (default: 0.1)

   -z <std::string>,  --outputWeightStructuresImage <std::string>
     Image specifying the the matrices weighting between plane, tube and
     point-like structures. This is applicable for sparse sliding organ
     registration only. This is in the space of the fixed image. Optional:
     allows you to save the weight image when providing an organ boundary
     surface. On later registrations, you can provide it instead of an
     organ boundary, so that it does not need to be recalculated.

   -x <std::string>,  --outputWeightRegularizationsImage <std::string>
     Image specifying the weights between the anisotropic diffusive
     regularization and the diffusive regularization, typically a function
     of distance to the organ boundary. This is in the space of the fixed
     image. Optional: allows you to save the weight image when providing an
     organ boundary surface. On later registrations, you can provide it
     instead of an organ boundary, so that it does not need to be
     recalculated.

   -v <std::string>,  --outputNormalVectorImage <std::string>
     Image specifying the normal vectors. This is in the space of the fixed
     image. Optional: allows you to save the normal vector image when
     providing an organ boundary surface. On later registrations, you can
     provide it instead of an organ boundary, so that it does not need to
     be recalculated. Gives the 0th column vector of the normal matrix if
     using the sparse registration.

   -o <std::string>,  --outputResampledMovingFileName <std::string>
     Resampled moving image to fixed image coordinate frame. Optional
     (specify an output deformation field or an output volume or both).

   -d <std::string>,  --outputDeformationField <std::string>
     Deformation field calculated that aligns the fixed and moving image.
     Maps positions from the fixed coordinate frame to the moving
     coordinate frame. Optional (specify an output deformation field or an
     output volume or both).

   --stoppingCriterionMask <std::string>
     Mask specifying which voxels should be used in the stopping criterion.
     Only pixels with value zero WILL be included in the metric computation
     and stopping criterion.

   --backgroundIntensity <double>
     Background intensity of the moving image. (default: 0)

   -q <std::string>,  --initialTransformImage <std::string>
     Initial transform for aligning the fixed and moving image, specified
     as a vector image. When applied to the moving image, should make it
     look closer to the fixed image. Optional. If both an 'initial
     transform' image and an 'initial transform' transform are given, the
     'initial transform' image will be used.

   -t <std::string>,  --initialTransform <std::string>
     Initial transform for aligning the fixed and moving image. When
     applied to the moving image, should make it look closer to the fixed
     image. Optional. If both an 'initial transform' image and an 'initial
     transform' transform are given, the 'initial transform' image will be
     used.

   -e <std::string>,  --inputWeightStructuresImage <std::string>
     Image specifying the the matrices weighting between plane, tube and
     point-like structures. This is applicable for sparse sliding organ
     registration only. This image should be in the space of the fixed
     image. Optional: supply a weight image or an organ boundary surface
     (and a lambda). If both are provided, the organ boundary surface is
     used.

   -w <std::string>,  --inputWeightRegularizationsImage <std::string>
     Image specifying the weights between the anisotropic diffusive
     regularization and the diffusive regularization, typically a function
     of distance to the organ boundary. This should be in the space of the
     fixed image. Optional: supply a weight image or an organ boundary
     surface (and a lambda). If both are provided, the organ boundary
     surface is used.

   -n <std::string>,  --inputNormalVectorImage <std::string>
     Image specifying the normal vectors. This should be in the space of
     the fixed image. Optional: supply a normal vector image or an organ
     boundary surface. If both are provided, the organ boundary surface is
     used.

   -p <std::string>,  --tubeSpatialObject <std::string>
     Filename of the tube spatial object (.tre). This should be in the
     space of the fixed image. Use for sparse anisotropic diffusion
     registration only.

   -b <std::string>,  --organBoundary <std::string>
     Filename of the organ boundary surface model. This should be in the
     space of the fixed image.

   -m <double>,  --maximumRMSError <double>
     If the RMS change in a registration iteration is less than the maximum
     RMS error threshold, the registration will be halted. Specify a larger
     value to halt faster. If using a multiresolution registration, the
     maximum RMS error condition will be tested at every level (i.e. will
     run at least one registration on each iteration). If zero, the RMS
     change stopping criterion is not used. (default: 0)

   --maximumTotalEnergyChange <double>
     If the total energy change summed over the stopping criterion
     evaluation period is less than the maximum total energy change
     threshold, then the registration will be halted. Specify a larger
     value to halt faster. If zero, the total energy change stopping
     criterion is not used. (default: 0)

   --stoppingCriterionPeriod <int>
     The number of iterations that elapse between evaluations of the total
     energy change stopping criterion. (default: 50)

   -k <std::vector<double>>,  --regularizationWeightings
      <std::vector<double>>
     Comma separated list of weightings to be applied to the regularization
     update term. The final update term will be ( itensityDistanceWeighting
     * intensityUpdateTerm ) + ( RegularizationWeighting *
     regularizationUpdateTerm ). Increase this value to increase the
     smoothness of the resulting displacement field. If using a
     multiresolution registration, you can set a different weighting for
     each level. If, on any multiresolution level, the current level is
     past the number of provided weights, the last weight will be used
     (allowing you to specify only one weight to be used on all levels).
     Default is 1.0 for each level. (default: 1.0)

   -s <double>,  --timestep <double>
     Time step duration. (default: 0.125)

   -i <std::vector<int>>,  --iterations <std::vector<int>>
     Comma separated list of iterations. The number of iterations specified
     dictates the number of levels of the multiresolution registration. The
     multiresolution shrink factors are halved in all three directions on
     each of the multiresolution levels. The registration will stop when
     either the maximum RMS error condition or the number of iterations
     condition is reached. (default: 20)

   --,  --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)  Fixed image to which to register.

   <std::string>
     (required)  Moving image.

   Author(s): Danielle F. Pace (Kitware)

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