rpyANTs (version 0.0.4)

correct_intensity: Truncate and correct 'MRI' intensity

Description

Uses ants.abp_n4 to truncate and correct intensity

Usage

correct_intensity(image, mask = NULL, intensity_truncation = c(0.025, 0.975))

Value

An 'ANTsImage' instance

Arguments

image

'MRI' image to be corrected, will be passed to as_ANTsImage

mask

binary mask image

intensity_truncation

numerical length of two, quantile probabilities to truncate.

Examples

if(interactive() && ants_available()) {
  ants <- load_ants()
  scale <- (0.1 + outer(
    seq(0, 1, length.out = 256)^6,
    seq(0, 1, length.out = 256)^2,
    FUN = "+"
  )) / 6
  img = ants$image_read(ants$get_ants_data('r16')) * scale

  corrected <- correct_intensity(img)

  pal <- gray.colors(255, start = 0)
  par(mfrow = c(1, 2), mar = c(0.1, 0.1, 2.1, 0.1),
      bg = "black", fg = "white")
  image(img[], asp = 1, axes = FALSE,
        col = pal, ylim = c(1, 0),
        main = "Original", col.main = "white")
  image(corrected[], asp = 1, axes = FALSE,
        col = pal, ylim = c(1, 0),
        main = "Corrected", col.main = "white")

}