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.

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")
# }