mincImage: Plot a slice from a MINC volume

In Mouse-Imaging-Centre/RMINC: Statistical Tools for Medical Imaging NetCDF (MINC) Files

Plot a slice from a MINC volume

Description

Calls the image plotting function from the base R graphics with some additional data munging to make it easy to work with MINC slices

Usage

mincImage(
  volume,
  dimension = 2,
  slice = NULL,
  low = min(volume, na.rm = TRUE),
  high = max(volume, na.rm = TRUE),
  reverse = FALSE,
  underTransparent = FALSE,
  col = gray.colors(255),
  add = FALSE,
  ...
)

Arguments

volume	a MINC volume as returned by mincArray
dimension	the dimension (1-3) to obtain the slice from
slice	the slice number
low	the low end of the range to plot. If not specified then it will be estimated based on the volume's histogram.
high	the high end of the range to plot. If not specified then it will be estimated based on the volume's histogram.
reverse	whether to look only at negative numbers.
underTransparent	whether to make anything below the low end of the range transparent.
col	a colour palette AKA look-up-table to colourize the slice intensities
add	whether to add the slice to the current plot device or open a new one before plotting
...	other parameters to pass on to the image function.

Details

You can get a fuller tutorial on how to use the visualization tools by executing the following command: file.show(system.file("doc/visualizationTutorial.html", package="RMINC"))

On certain systems the slices are plotted with a reflected y-axis. To fix this configure options(RMINC_flip_image = TRUE)

Examples

## Not run: 
mincImage(mincArray(anatVol), slice=100, col=gray.colors(255))
mincImage(mincArray(vs, 6), slice=100, col=rainbow(255), 
          underTransparent = T, low=2, high=6, add=T)

## End(Not run)

Mouse-Imaging-Centre/RMINC documentation built on Feb. 24, 2025, 1:22 a.m.