mincPlotSliceSeries: MINC Slice Series

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

MINC Slice Series

Description

Plot a series of slices through a minc volume on a given dimension. Optionally superimpose statistics, and or include a locator contour to show where slices are.

Usage

mincPlotSliceSeries(
  anatomy,
  statistics = NULL,
  dimension = 2,
  mfrow = c(4, 5),
  low = NULL,
  high = NULL,
  anatLow = NULL,
  anatHigh = NULL,
  col = heat.colors(255),
  anatCol = gray.colors(255, start = 0),
  begin = 1,
  end = (dim(anatomy)[dimension] - 1),
  symmetric = FALSE,
  legend = NULL,
  locator = !is.null(legend),
  plottitle = NULL,
  indicatorLevels = NULL,
  discreteStats = FALSE,
  legendHeight = 0.5
)

Arguments

anatomy	A minc array of the anatomy volume to plot
statistics	optional statistics or label file to overlay on anatomy slices
dimension	integer denoting which dimension to slice across
mfrow	A 2 element vector of the form c(rows, columns) indicating the number and position of slices to draw - slices are added by rows
low	the minimum statistic to plot, taken from histogram if not supplied and not discreteStats, otherwise the minimum statistic
high	the maximum statistic to plot, taken from histogram if not supplied and not discreteStats, otherwise the maximum statistic
anatLow	the minimum anatomy intensity to plot
anatHigh	the maximum antomy intensity to plot
col	colours for statistics or for the anatomy if statistics are not passed
anatCol	colours for the
begin	the first slice to plot, defaults to 1
end	the last slice to plot, defaults to the last slice
symmetric	whether the statistics are symmetric (such as for t-statistics)
legend	an optional string to name the legend, indicating desire for a legend (or not)
locator	whether or not to draw the locator, defaults to whether or not you requested a legend
plottitle	the title of the plot if desired
indicatorLevels	numeric vector indicating where to draw slice lines on the locator, defaults to every slice
discreteStats	Whether stats are discrete values and should should not have their range taken from their histogram if unsupplied.
legendHeight	What vertical fraction of the figure should the legend occupy

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: 
mincPlotSliceSeries(mincArray(anatVol),           # the anatomical volume
                    mincArray(vs, "tvalue-SexM"), # pull out one column of the stats
                    anatLow=700, anatHigh=1400,   # set anatomy thresholds
                    low=2.5, high=10,             # set stats thresholds
                    symmetric=T,                  # show separate upper and lower
                    begin=25, end=-25  ,          # remove slices from both sides  
                    legend="t-statistics")

## End(Not run)

Mouse-Imaging-Centre/RMINC documentation built on Nov. 12, 2022, 1:50 p.m.