Apply transforms to images.

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.

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

Shrinidhi KL, Avants BB

Examples


# will give the full form of help
antsApplyTransforms("-h")
#> NULL
# 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
)
#> antsRegistration -d 2 -r [0x600002a9d340,0x600002a9f460,1] -m mattes[0x600002a9d340,0x600002a9f460,1,32,regular,0.2] -t Affine[0.25] -c 2100x1200x1200x0 -s 3x2x1x0 -f 4x2x2x1 -x [NA,NA] -m mattes[0x600002a9d340,0x600002a9f460,1,32] -t SyN[0.2,3,0] -c [ 40x20x0 ,1e-7,8] -s 2x1x0 -f 4x2x1 -u 0 -z 1 -o [/tmp//Rtmpx3PKqM/filebbf73809607,0x600002a9f8b0,0x600002a9f2e0] -x [NA,NA] --float 1 --random-seed 1 --write-composite-transform 0 -v 1 
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$fwdtransforms[2],
  whichtoinvert = 1, verbose = TRUE
)
#>  [1] "-d"                                                    
#>  [2] "2"                                                     
#>  [3] "-i"                                                    
#>  [4] "<pointer: 0x600002a9ef60>"                             
#>  [5] "-o"                                                    
#>  [6] "<pointer: 0x600002ab51f0>"                             
#>  [7] "-r"                                                    
#>  [8] "<pointer: 0x600002ab6920>"                             
#>  [9] "-n"                                                    
#> [10] "linear"                                                
#> [11] "-t"                                                    
#> [12] "[/tmp//Rtmpx3PKqM/filebbf738096070GenericAffine.mat,1]"
cfile <- antsApplyTransforms(
  fixed = fixed, moving = moving,
  transformlist = mytx$fwdtransforms,
  compose = tempfile()
)
cimg <- antsImageRead(cfile)
cout <- antsApplyTransforms(
  fixed = fixed, moving = moving,
  transformlist = cimg
)
#> Warning: transformlist is an antsImage, creating a temporary file
testthat::expect_error(
  antsApplyTransforms(
    fixed = fixed, moving = moving,
    transformlist = cimg, whichtoinvert = 1
  ), "nnot invert transform"
)
#> Warning: transformlist is an antsImage, creating a temporary file
testthat::expect_error(
  antsApplyTransforms(
    fixed = fixed, moving = moving,
    transformlist = cimg, whichtoinvert = c(1, 2)
  ), "same length"
)
#> Warning: transformlist is an antsImage, creating a temporary file
testthat::expect_error(antsApplyTransforms(
  fixed = fixed, moving = moving,
  transformlist = ""
))

Arguments

Value

See also

Author

Examples