fitTransformToPairedPoints: fitTransformToPairedPoints

In stnava/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

fitTransformToPairedPoints

Description

Estimate a transform using paired point sets. An ANTsR transform is returned.

Usage

fitTransformToPairedPoints(
  movingPoints,
  fixedPoints,
  transformType = "affine",
  regularization = 0.000001,
  domainImage = NULL,
  numberOfFittingLevels = 4,
  meshSize = 1,
  splineOrder = 3,
  enforceStationaryBoundary = TRUE,
  displacementWeights = NULL,
  numberOfCompositions = 10,
  compositionStepSize = 0.5,
  sigma = 0,
  convergenceThreshold = 0.000001,
  numberOfTimeSteps = 2,
  numberOfIntegrationSteps = 100,
  rasterizePoints = FALSE,
  verbose = FALSE
)

Arguments

movingPoints	Moving points specified in physical space as a n x d matrix where n is the number of points and d is the dimensionality.
fixedPoints	Fixed points specified in physical space as a n x d matrix where n is the number of points and d is the dimensionality.
transformType	'rigid', 'similarity', 'affine', 'bspline', 'tps', 'diffeo', 'syn', 'tv', or 'time-varying'.
regularization	Ridge penalty in [0,1] for linear transforms.
domainImage	Defines physical domain of the B-spline transform. Must be defined for nonlinear transforms.
numberOfFittingLevels	Integer specifying the number of fitting levels for the B-spline interpolation of the displacement field.
meshSize	Defines the mesh size at the initial fitting level for the B-spline interpolation of the displacement field.
splineOrder	Spline order of the B-spline displacement field.
enforceStationaryBoundary	Ensure no displacements on the image boundary (B-spline only).
displacementWeights	Defines the individual weighting of the corresponding scattered data value. Default = None meaning all displacements are weighted the same.
numberOfCompositions	Total number of compositions for the diffeomorphic transform.
compositionStepSize	Scalar multiplication factor of the weighting of the update field for the diffeomorphic transforms.
sigma	Gaussian smoothing standard deviation of the update field (in mm).
convergenceThreshold	Composition-based convergence parameter for the diffeomorphic transforms using a window size of 10 values.
numberOfTimeSteps	Time-varying velocity field parameter.
numberOfIntegrationSteps	Number of steps used for integrating the velocity field.
rasterizePoints	Use nearest neighbor rasterization of points for estimating update field (potential speed-up).
verbose	Print progress to the screen.

Value

object containing ANTsR transform, error, and scale (or displacement field)

Author(s)

B Avants, N Tustison

Examples

fixed <- matrix(c(50, 50, 200, 50, 50, 200), ncol = 2, byrow = TRUE)
moving <- matrix(c(50, 50, 50, 200, 200, 200), ncol = 2, byrow = TRUE)

# Affine transform
xfrm <- fitTransformToPairedPoints(moving, fixed, transformType = "Affine", 
regularization = 0)
params <- getAntsrTransformParameters(xfrm)

# Rigid transform
xfrm <- fitTransformToPairedPoints(moving, fixed, transformType = "Rigid", 
regularization = 0)
params <- getAntsrTransformParameters(xfrm)

# Similarity transform
xfrm <- fitTransformToPairedPoints(moving, fixed, 
transformType = "Similarity", regularization = 0)
params <- getAntsrTransformParameters(xfrm)

# B-spline transform
domainImage <- antsImageRead(getANTsRData("r16"))
xfrm <- fitTransformToPairedPoints(moving, fixed, 
transformType = "Bspline", domainImage = domainImage, 
numberOfFittingLevels = 5)

stnava/ANTsR documentation built on April 16, 2024, 12:17 a.m.