rpyANTs (version 0.0.4)

ants_apply_transforms: Apply a transform list to map an image from one domain to another

Description

See ants$apply_transforms for more details.

Usage

ants_apply_transforms(
  fixed,
  moving,
  transformlist,
  interpolator = c("linear", "nearestNeighbor", "gaussian", "genericLabel", "bSpline",
    "cosineWindowedSinc", "welchWindowedSinc", "hammingWindowedSinc",
    "lanczosWindowedSinc"),
  imagetype = 0L,
  whichtoinvert = NULL,
  compose = NULL,
  defaultvalue = 0,
  verbose = FALSE,
  ...
)

Value

Transformed image. The image will share the same space as fixed.

Arguments

fixed

fixed image defining domain into which the moving image is transformed

moving

moving image to be mapped to fixed space

transformlist

list of strings (path to transforms) generated by ants_registration where each transform is a file name

interpolator

how to interpolate the image; see 'Usage'

imagetype

integer: 0 (scalar), 1 (vector), 2 (tensor), 3 (time-series), used when the fixed and moving images have different mode (dimensions)

whichtoinvert

either NULL, None ('Python'), or a vector of logical with same length as transformlist; print ants$apply_transforms to see detailed descriptions

compose

optional character pointing to a valid file location

defaultvalue

numerical value for mappings outside the image domain

verbose

whether to verbose application of transform

...

must be named arguments passing to further methods

See Also

print(ants$apply_transforms)

Examples

if(interactive() && ants_available()) {
  ants <- load_ants()
  fixed <- as_ANTsImage( ants$get_ants_data('r16') )
  moving <- as_ANTsImage( ants$get_ants_data('r64') )
  fixed <- ants_resample_image(fixed, c(64, 64), TRUE, "linear")
  moving <- ants_resample_image(moving, c(64,64), TRUE, "linear")

  mytx <- ants_registration(fixed = fixed,
                            moving = moving,
                            type_of_transform = 'SyN')
  mywarpedimage <- ants_apply_transforms(
    fixed = fixed,
    moving = moving,
    transformlist = mytx$fwdtransforms
  )

  par(mfrow = c(1,3), mar = c(0,0,3,0))
  pal <- gray.colors(256)
  image(fixed[], asp = 1, axes = FALSE, col = pal,
        ylim = c(1, 0), main = "Reference")
  image(moving[], asp = 1, axes = FALSE, col = pal,
        ylim = c(1, 0), main = "Moving")
  image(mywarpedimage[], asp = 1, axes = FALSE, col = pal,
        ylim = c(1, 0), main = "Moving reg+resamp into Reference")
}