n3BiasFieldCorrection2: N3 Bias field correction

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

N3 Bias field correction

Description

Perform N3 bias field correction on the given image

Usage

n3BiasFieldCorrection2(
  img,
  mask,
  rescaleIntensities = FALSE,
  shrinkFactor = 4,
  convergence = list(iters = 50, tol = 0.0000001),
  splineParam = 200,
  numberOfFittingLevels = 4,
  weightMask = NULL,
  returnBiasField = FALSE,
  verbose = FALSE
)

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, maximum number of iterations 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 is a mesh size of 1 per dimension.
numberOfFittingLevels	Parameter controlling number of fitting levels.
weightMask	antsImage of weight mask
returnBiasField	bool, return the field instead of the corrected image.
verbose	enables verbose output.

Value

bias corrected image or bias field

Author(s)

Avants BB, Tustison NJ

Examples

dims <- c(50, 50)
img <- makeImage(imagesize = dims, rnorm(prod(dims)))
n3img <- n3BiasFieldCorrection2(img)
n3img <- n3BiasFieldCorrection2(img, mask = img > 0)
testthat::expect_error(n3BiasFieldCorrection2(img, weightMask = "somepath"))
testthat::expect_error(n3BiasFieldCorrection2(img, splineParam = rep(200, 3)))
# n3img<-n3BiasFieldCorrection2(img, splineParam = c(200, 20)) # long running

rm(img)
gc()
rm(n3img)
gc()
fname <- getANTsRData("r16")
in_img <- antsImageRead(fname)
n3 <- n3BiasFieldCorrection2(in_img)
rm(n3)
gc()
mask <- in_img > 0
mask2 <- antsImageClone(mask, out_pixeltype = "float")
# fails
mask
sum(mask)
## Not run: 
n3 <- n3BiasFieldCorrection2(in_img, mask = mask, verbose = TRUE)
# fails
n3 <- n3BiasFieldCorrection2(in_img, mask = mask2)

## End(Not run)

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