smooth_image: Gaussian smooth image using ANTsR

In muschellij2/extrantsr: Extra Functions to Build on the 'ANTsR' Package

Description

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

Usage

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)
})

muschellij2/extrantsr documentation built on July 27, 2021, 7:41 a.m.