antsApplyTransforms: Apply transforms to images.

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

Apply transforms to images.

Description

Apply a transform list to map an image from one domain to another. In image registration, one computes mappings between (usually) pairs of images. These transforms are often a sequence of increasingly complex maps, e.g. from translation, to rigid, to affine to deformation. The list of such transforms is passed to this function to interpolate one image domain into the next image domain, as below. The order matters strongly and the user is advised to familiarize with the standards established in examples.

Usage

antsApplyTransforms(
  fixed,
  moving,
  transformlist = "",
  interpolator = c("linear", "nearestNeighbor", "multiLabel", "gaussian", "bSpline",
    "cosineWindowedSinc", "welchWindowedSinc", "hammingWindowedSinc",
    "lanczosWindowedSinc", "genericLabel"),
  imagetype = 0,
  whichtoinvert = NA,
  compose = NA,
  verbose = FALSE,
  ...
)

Arguments

fixed	fixed image defining domain into which the moving image is transformed.
moving	moving image to be mapped to fixed space.
transformlist	character vector of transforms generated by antsRegistration where each transform is a filename.
interpolator	Choice of interpolator. Supports partial matching. linear nearestNeighbor multiLabel for label images but genericlabel is preferred gaussian bSpline cosineWindowedSinc welchWindowedSinc hammingWindowedSinc lanczosWindowedSinc genericLabel use this for label images
imagetype	choose 0/1/2/3 mapping to scalar/vector/tensor/time-series
whichtoinvert	optional list of booleans, same length as transforms. whichtoinvert[i] is TRUE if transformlist[i] is a matrix, and the matrix should be inverted. If transformlist[i] is a warp field, whichtoinvert[i] must be FALSE. If the transform list is a matrix followed by a warp field, whichtoinvert defaults to c(TRUE,FALSE). Otherwise it defaults to rep(FALSE, length(transformlist)).
compose	if it is a character string pointing to a valid file location, this will force the function to return a composite transformation filename.
verbose	print command and run verbose application of transform.
...	extra parameters

Value

an antsImage or transformation filename is output. 1 – Failure

Author(s)

Shrinidhi KL, Avants BB

See Also

antsRegistration

Examples

# will give the full form of help
antsApplyTransforms("-h")
# see antsRegistration
# example 1 - simplified
fixed <- ri(1)
moving <- ri(2)
fixed <- resampleImage(fixed, c(64, 64), 1, 0)
moving <- resampleImage(moving, c(68, 68), 1, 0)
mytx <- antsRegistration(
  fixed = fixed, moving = moving,
  typeofTransform = "SyN", verbose = TRUE, printArgs = TRUE
)
mywarpedimage <- antsApplyTransforms(
  fixed = fixed, moving = moving,
  transformlist = mytx$fwdtransforms
)
testthat::expect_true(antsImagePhysicalSpaceConsistency(mywarpedimage, fixed))
invwarped_image <- antsApplyTransforms(
  fixed = moving, moving = fixed,
  transformlist = mytx$invtransforms
)
testthat::expect_true(antsImagePhysicalSpaceConsistency(invwarped_image, moving))
# full access via listing the inputs in standard ANTs format

res1 <- antsApplyTransforms(
  fixed = fixed, moving = moving,
  transformlist = mytx$fwdtransforms[2],
  whichtoinvert = 1, verbose = TRUE
)
cfile <- antsApplyTransforms(
  fixed = fixed, moving = moving,
  transformlist = mytx$fwdtransforms,
  compose = tempfile()
)
cimg <- antsImageRead(cfile)
cout <- antsApplyTransforms(
  fixed = fixed, moving = moving,
  transformlist = cimg
)
testthat::expect_error(
  antsApplyTransforms(
    fixed = fixed, moving = moving,
    transformlist = cimg, whichtoinvert = 1
  ), "nnot invert transform"
)
testthat::expect_error(
  antsApplyTransforms(
    fixed = fixed, moving = moving,
    transformlist = cimg, whichtoinvert = c(1, 2)
  ), "same length"
)
testthat::expect_error(antsApplyTransforms(
  fixed = fixed, moving = moving,
  transformlist = ""
))

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