Gaussian smooth image using ANTsR — smooth

This function calls smoothIamge to smooth an image and either saves the image or returns an object of class nifti

smooth_image(
  file,
  sigma = 10,
  mask = NULL,
  smooth_mask = TRUE,
  smoothed_mask = NULL,
  verbose = TRUE,
  retfile = FALSE,
  ...
)

Arguments

file	(character) image to be smoothed
sigma	(numeric) sigma (in mm) of Gaussian kernel for smoothing
mask	(character) optional mask given for image
smooth_mask	(logical) Smooth mask? If TRUE, the masked image will be divided by the smoothed mask.
smoothed_mask	(character or antsImage) If specified and `smooth_mask = TRUE`, then will use this as the smoothed mask for division.
verbose	(logical) print out command before running
retfile	logical to indicate if an `antsImage` should be returned (useful for chaining)
...	additional arguments passed to `smoothImage`.

Value

Object of class nifti

Examples

system.time({
library(oro.nifti)
dims = c(50, 50, 50)
x = array(rnorm(prod(dims)), dim = dims)
img = nifti(x, dim= dims,
datatype = convert.datatype()$FLOAT32, cal.min = min(x), 
cal.max = max(x), pixdim = rep(1, 4))
s.img = smooth_image(img, sigma = 3, sigmaInPhysicalCoordinates = TRUE)
})
#>    user  system elapsed 
#>   0.760   0.008   0.767