Plot slices of volume

Usage

plot_slices(
  volume,
  overlays = NULL,
  transform = NULL,
  positions = NULL,
  zoom = 1,
  pixel_width = 0.5,
  col = c("black", "white"),
  normalize = NULL,
  zclip = NULL,
  overlay_alpha = 0.3,
  zlim = normalize,
  main = "",
  title_position = c("left", "top"),
  fun = NULL,
  nc = NA,
  which = NULL,
  ...
)

Arguments

volume: path to volume (underlay)
overlays: images to overlay on top of the underlay, can be either a vector of paths to the overlay volume images, or a sequence of named lists. Each list item has 'volume' (path to the volume) and 'color' (color of the overlay)
transform: rotation of the volume in scanner 'RAS' space
positions: vector of length 3 or matrix of 3 columns, the 'RAS' position of cross-hairs
zoom: zoom-in radio, default is 1
pixel_width: output image pixel resolution; default is 0.5, one pixel is 0.5 millimeters wide
col: color palette, can be a sequence of colors
normalize: range for volume data to be normalized; either NULL (no normalize) or a numeric vector of length two
zclip: clip image densities; if specified, values outside of this range will be clipped into this range
overlay_alpha: transparency of the overlay; default is 0.3
zlim: image plot value range, default is identical to normalize
main: image titles
title_position: title position; choices are "left" or "top"
fun: function with two arguments that will be executed after each image is drawn; can be used to draw cross-hairs or annotate each image
nc: number of "columns" in the plot when there are too many positions, must be positive integer; default is NA (automatically determined)
which: which plane to plot; default is NULL, which will trigger new plots and add titles; set to 1 for 'Axial' plane, 2 for 'Sagittal', and 3 for 'Coronal'.
...: additional arguments passing into image

Value

Nothing