viewer: A simple interactive viewer for MriImage objects

In tractor.base: Read, Manipulate and Visualise Magnetic Resonance Images

A simple interactive viewer for MriImage objects

Description

The viewImages function provides a simple interactive viewer for MriImage objects. 3D and 4D images may be used.

Usage

defaultInfoPanel(point, data, imageNames)

timeSeriesPanel(point, data, imageNames)

polarPlotPanel(point, data, imageNames, directions, bValues = NULL)

viewImages(images, colourScales = NULL, point = NULL, interactive = TRUE,
  crosshairs = TRUE, orientationLabels = TRUE, fixedWindow = TRUE,
  indexNames = NULL, infoPanel = defaultInfoPanel, ...)

Arguments

point	For viewImages, a length 3 integer vector giving the initial location of the crosshairs, in voxels. For info panel functions, the current location of the crosshairs.
data	A list giving the data value(s) at the current crosshair location in each image displayed. Typically numeric, but in principle may be of any mode, and will be character mode when indexNames is not NULL.
imageNames	A character vector giving a name for each image displayed.
directions	A matrix of 3D acquisition direction vectors, one per row.
bValues	A vector of b-values, if the image is diffusion-weighted.
images	An MriImage object, or list of MriImage objects.
colourScales	A list of colour scales to use for each image, which will be recycled to the length of images. See getColourScale for details. The default is to use greyscale.
interactive	A single logical value. If TRUE, the plot is interactive.
crosshairs	A single logical value. If TRUE, the crosshairs are displayed.
orientationLabels	A single logical value. If TRUE, orientation labels are displayed.
fixedWindow	A single logical value. If TRUE, each image is windowed globally, rather than for each slice.
indexNames	A list whose elements are either NULL or a named character vector giving the names associated with each index in the image.
infoPanel	A function with at least three arguments, which must plot something to fill the bottom-right panel of the viewer after each change of crosshair location. The three mandatory arguments correspond to the current location in the image, the image values at that location, and the names of each image. The defaultInfoPanel and timeSeriesPanel functions are valid examples.
...	Additional arguments to infoPanel.

Value

These functions are called for their side effects.

Note

The defaultInfoPanel and timeSeriesPanel functions are not intended to be called directly. They are simple examples of valid values for the infoPanel argument to viewImages.

Author(s)

Jon Clayden

References

Please cite the following reference when using TractoR in your work:

J.D. Clayden, S. Muñoz Maniega, A.J. Storkey, M.D. King, M.E. Bastin & C.A. Clark (2011). TractoR: Magnetic resonance imaging and tractography with R. Journal of Statistical Software 44(8):1-18. https://www.jstatsoft.org/v44/i08/.

See Also

getColourScale

tractor.base documentation built on Aug. 24, 2022, 5:06 p.m.