rpyANTs (version 0.0.4)

ants_plot: Plot single 'ANTsImage'

Description

Plot single 'ANTsImage'

Usage

ants_plot(
  image,
  overlay = NULL,
  blend = FALSE,
  alpha = 1,
  cmap = "Greys_r",
  overlay_cmap = "turbo",
  overlay_alpha = 0.9,
  vminol = NULL,
  vmaxol = NULL,
  cbar = FALSE,
  cbar_length = 0.8,
  cbar_dx = 0,
  cbar_vertical = TRUE,
  axis = 0,
  nslices = 12,
  slices = NULL,
  ncol = NULL,
  slice_buffer = NULL,
  black_bg = TRUE,
  bg_thresh_quant = 0.01,
  bg_val_quant = 0.99,
  domain_image_map = NULL,
  crop = FALSE,
  scale = FALSE,
  reverse = FALSE,
  title = "",
  title_fontsize = 20,
  title_dx = 0,
  title_dy = 0,
  filename = NULL,
  dpi = 500,
  figsize = 1.5,
  reorient = TRUE,
  resample = TRUE,
  force_agg = FALSE,
  close_figure = TRUE
)

Value

Nothing

Arguments

image

'ANTsImage', or something can be converted to 'ANTsImage'

overlay

overlay 'ANTsImage', can be NULL, optional

blend

whether to blend image with overlay; default is false

cmap, alpha

image color map and transparency

overlay_cmap, overlay_alpha

overlay color map and transparency

vminol, vmaxol

I could not find its usage

cbar

whether to draw color legend

cbar_length, cbar_dx, cbar_vertical

legend position and size

axis

see 'Details'

nslices, slices, ncol

controls slice to show

slice_buffer

performance

black_bg, bg_thresh_quant, bg_val_quant

controls background

domain_image_map

optional 'ANTsImage'

crop, scale, reverse

whether to crop, scale, or reverse the image according to background

title, title_fontsize, title_dx, title_dy

image title

filename, dpi, figsize

needed when saving to file

reorient

whether to reorient to 'LAI' before plotting; default is true

resample

whether to resample

force_agg

whether to force graphic engine to use 'agg' device; default is false

close_figure

whether to close figure when returning the function

Details

By default, images will be reoriented to 'LAI' orientation before plotting. So, if axis=0, the images will be ordered from the left side of the brain to the right side of the brain. If axis=1, the images will be ordered from the anterior (front) of the brain to the posterior (back) of the brain. And if axis=2, the images will be ordered from the inferior (bottom) of the brain to the superior (top) of the brain.

Examples

if(interactive() && ants_available()) {
  ants <- load_ants()
  img <- ants$image_read(ants$get_ants_data('mni'))

  ants_plot(
    img, nslices = 12, black_bg = FALSE,
    bg_thresh_quant = 0.05, bg_val_quant = 1.0, axis = 2,
    cbar = TRUE, crop = TRUE, reverse = TRUE, cbar_vertical = FALSE,
    ncol = 4, title = "Axial view of MNI brain"
  )
}