n4BiasFieldCorrection: N4 bias field correction

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

N4 bias field correction

Description

Perform N4 bias field correction on the given image

Usage

n4BiasFieldCorrection(
  img,
  mask,
  rescaleIntensities = FALSE,
  shrinkFactor = 4,
  convergence = list(iters = c(50, 50, 50, 50), tol = 0.0000001),
  splineParam = 200,
  returnBiasField = FALSE,
  verbose = FALSE,
  weightMask = NULL
)

Arguments

img	input antsImage
mask	input mask, if one is not passed one will be made
rescaleIntensities	At each iteration, a new intensity mapping is calculated and applied but there is nothing which constrains the new intensity range to be within certain values. The result is that the range can "drift" from the original at each iteration. This option rescales to the [min,max] range of the original image intensities within the user-specified mask. A mask is required to perform rescaling. Default is FALSE in ANTsR/ANTsPy but TRUE in ANTs.
shrinkFactor	Shrink factor for multi-resolution correction, typically integer less than 4.
convergence	List of: iters, vector of maximum number of iterations for each shrinkage factor, and tol, the convergence tolerance. Default tolerance is 1e-7 in ANTsR/ANTsPy but 0.0 in ANTs.
splineParam	Parameter controlling number of control points in spline. Either single value, indicating how many control points, or vector with one entry per dimension of image, indicating the spacing in each direction. Default in ANTsR/ANTsPy is 200 mm per mesh element in each dimension. The ANTs default is a mesh size of 1 per dimension.
returnBiasField	bool, return the field instead of the corrected image.
verbose	enables verbose output.
weightMask	antsImage of weight mask

Value

bias corrected image or bias field

Author(s)

BB Avants

Examples

dims <- c(50, 50)
img <- makeImage(imagesize = dims, rnorm(prod(dims)))
n4img <- n4BiasFieldCorrection(img)
n4img <- n4BiasFieldCorrection(img, mask = img > 0)
testthat::expect_error(n4BiasFieldCorrection(img, weightMask = "somepath"))
testthat::expect_error(n4BiasFieldCorrection(img, splineParam = rep(200, 3)))
n4img <- n4BiasFieldCorrection(img, splineParam = c(200, 20))

rm(img)
gc()
rm(n4img)
gc()
fname <- getANTsRData("r16")
in_img <- antsImageRead(fname)
n4 <- n4BiasFieldCorrection(in_img)
rm(n4)
gc()
mask <- in_img > 0
mask2 <- antsImageClone(mask, out_pixeltype = "float")
# fails
mask
sum(mask)
## Not run: 
n4 <- n4BiasFieldCorrection(in_img, mask = mask, verbose = TRUE)
# fails
n4 <- n4BiasFieldCorrection(in_img, mask = mask2)

## End(Not run)

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