labelImageRegistration: Perform label image registration.

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

Perform label image registration.

Description

Perform pairwise registration using fixed and moving sets of label images (and, optionally, sets of corresponding intensity images).

Usage

labelImageRegistration(
  fixedLabelImages,
  movingLabelImages,
  fixedIntensityImages = NULL,
  movingIntensityImages = NULL,
  fixedMask = NULL,
  movingMask = NULL,
  initialTransforms = "affine",
  typeOfLinearTransform = NULL,
  typeOfDeformableTransform = "antsRegistrationSyNQuick[so]",
  labelImageWeighting = 1,
  outputPrefix = "",
  randomSeed = NULL,
  verbose = FALSE
)

Arguments

fixedLabelImages	A single (or set of) fixed label image(s).
movingLabelImages	A single (or set of) moving label image(s).
fixedIntensityImages	Optional—a single (or set of) fixed intensity image(s).
movingIntensityImages	Optional—a single (or set of) moving intensity image(s).
fixedMask	Defines region for similarity metric calculation in the space of the fixed image.
movingMask	Defines region for similarity metric calculation in the space of the moving image.
initialTransforms	If specified, there are two options: 1) Use label images with the centers of mass to a calculate linear transform of type 'identity', 'rigid', 'similarity', 'affine'. 2) Specify a list of transform files, e.g., the output of antsRegistration.
typeOfLinearTransform	Use label images with the centers of mass to a calculate linear transform of type 'identity', 'rigid', 'similarity', 'affine'. Deprecated- subsumed by 'initialTransforms'.
typeOfDeformableTransform	Only works with deformable-only transforms, specifically the family of antsRegistrationSyN*[so] or antsRegistrationSyN*[bo] transforms. See 'typeOfTransform' in antsRegistration. Additionally, one can use a list to pass a more tailored deformable-only transform optimization using SyN or BSplineSyN transforms. The order of parameters in the list would be 1) transform specification, i.e. "SyN" or "BSplineSyN", 2) gradient (real), 3) intensity metric (string), 4) intensity metric parameter (real), 5) convergence iterations per level (vector) 6) smoothing factors per level (tuple), 7) shrink factors per level (vector). An example would typeOfDeformableTransform = list("SyN", 0.2, "CC", 4, c(100,50,10), c(2,1,0), c(4,2,1)).
labelImageWeighting	Float or vector of floats giving the relative weighting for the label images.
outputPrefix	String definining the output prefix for the filenames of the output transform files.
randomSeed	Definition for deformable registration.
verbose	Print progress to the screen.

Value

outputs a list containing:

fwdtransforms:

Transforms to move from moving to fixed image.

invtransforms:

Transforms to move from fixed to moving image.

Output of 1 indicates failure.

Author(s)

Tustison NJ

Examples

## Not run: 
r16 <- antsImageRead( getANTsRData( "r16" ) )
r16Seg1 <- thresholdImage( r16, "Kmeans", 3 ) - 1
r16Seg2 <- thresholdImage( r16, "Kmeans", 5 ) - 1
r64 <- antsImageRead( getANTsRData( "r64" ) )
r64Seg1 <- thresholdImage( r64, "Kmeans", 3 ) - 1
r64Seg2 <- thresholdImage( r64, "Kmeans", 5 ) - 1
reg <- labelImageRegistration( list( r16Seg1, r16Seg2 ),
                                     list( r64Seg1, r64Seg2 ),  
                                     fixedIntensityImages = r16,
                                     movingIntensityImages = r64,
                                     initialTransforms = 'affine',
                                     typeOfDeformableTransform = 'antsRegistrationSyNQuick[bo]',
                                     labelImageWeighting = c( 1.0, 2.0 ),
                                     verbose = TRUE )

## End(Not run)

stnava/ANTsR documentation built on April 13, 2025, 4:10 a.m.