Calls the image plotting function from the base R graphics with
some additional data munging to make it easy to work with MINC slices
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, ...)
| volume | a MINC volume as returned by |
|---|---|
| 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 |
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)
# 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) # }