visualisation: Visualise MriImage objects

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

Visualise MriImage objects

Description

Visualise MriImage objects noninteractively using an R graphics device. See viewImages for an interactive alternative. These functions create 2D visualisations of 3D images by slicing or maximum intensity projection.

Usage

createSliceGraphic(image, x = NA, y = NA, z = NA,
  device = c("internal", "png"), colourScale = 1, add = FALSE,
  file = NULL, zoomFactor = 1, windowLimits = NULL)

createProjectionGraphic(image, axis, device = c("internal", "png"),
  colourScale = 1, add = FALSE, file = NULL, zoomFactor = 1,
  windowLimits = NULL)

createContactSheetGraphic(image, axis, device = c("internal", "png"),
  colourScale = 1, add = FALSE, file = NULL, zoomFactor = 1,
  windowLimits = NULL, clearance = NULL, nColumns = NULL)

Arguments

image	An MriImage object.
x, y, z	Integer vectors, each of length 1. Exactly one of these must be specified to indicate the plane of interest.
device	Either "internal" for display on the default graphics device, or "png" for creating PNG format image file(s). Abbreviations are fine.
colourScale	A colour scale definition, of the sort generated by getColourScale.
add	Overlay the graphic on a previous one. Used only when device is "internal".
file	A file name, to be used when device is "png".
zoomFactor	Factor by which to enlarge the image. Applies only when device is "png".
windowLimits	Numeric vector of length 2 giving the limits of the colour scale, or NULL for limits matching the range of the image data. Passed as the zlim argument to image.
axis	A vector of axes along which slice/projection images should be created. 1 is left-right, 2 is anterior-posterior, 3 is superior-inferior.
clearance	Number of voxels' clearance to leave around each slice image in the contact sheet. Passed to trimMriImage.
nColumns	Number of slices per row in the contact sheet grid. If NULL, the function will aim for a square grid.

Value

These functions are called for their side effects.

Note

When the device option is set to "png", the "png" and "mmand" packages are required by these functions.

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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.18637/jss.v044.i08")}.

See Also

See viewImages for an interactive alternative, and getColourScale for details of how colour scales are specified. Also image, which is used as the underlying plot function.

tractor.base documentation built on May 29, 2024, 7:58 a.m.