plot-methods {dti}R Documentation

Methods for Function ‘plot’ in Package ‘dti’

Description

Visualization of objects of class "dtiData", "dtiIndices" and class "dtiTensor"

Usage

  ## S4 method for signature 'dtiData':
  plot(x, y, slice=1, gradient=NULL, view= "axial", show=TRUE, density=FALSE, xind=NULL, yind=NULL, zind=NULL, mar=c(3,3,3,.3), mgp=c(2,1,0), ...)
  ## S4 method for signature 'dtiTensor':
  plot(x, y, slice=1, view= "axial", method=1, quant=0, minanindex=NULL, show=TRUE, contrast.enh=1, what="FA", xind=NULL, yind=NULL, zind=NULL, mar=c(3,3,3,.3), mgp=c(2,1,0), ...)
  ## S4 method for signature 'dtiIndices':
  plot(x, y, slice=1, view="axial", quant=0, minanindex=NULL, show=TRUE, density=FALSE, contrast.enh=1,what="FA", qrange=c(.01,.99), xind=NULL, yind=NULL, zind=NULL, mar=c(2,2,2,.2), mgp=c(2,1,0), ...)

Arguments

x Object of class "dtiIndices", "dtiData" or "dtiTensor"
y Not used
slice Slice number
view Choose "sagittal", "coronal", or "axial" view here
gradient Index of data cube to plot. Defaults to the first S0 image.
method Method for color coding tensor indices.
quant If is.null(minanindex) specify minanindex as corresponding quantile of the fractal anisotropy (FA) index.
minanindex Display only information for voxel with FA>minanindex
show Visualize information in a graphics device (for classes "dtiData" and "dtiIndices" only).
density Show density of S0(Sb)-values (for class "dtiData") or densities of fractal anisotropy (FA) or geodesic anisotropy (GA) ( for class "dtiIndices").
contrast.enh Enhance image contrast using min(1,x$anindex/contrast.enh instead of the anisotropy index itself. Effective values are within the interval (0,1).
what If what="GA" use geodesic anisotropy (GA) instead of fractional anisotropy (FA).
mar Graphical parameter for par.
mgp Graphical parameter for par.
qrange Cut image intensity to these quantiles to avoid that outliers determine the dynamic range of the image.
xind If provided restrict display to indices specified in xind for x-direction.
yind If provided restrict display to indices specified in yind for y-direction.
zind If provided restrict display to indices specified in zind for z-direction.
... currently not used

Methods

x = "ANY"
Generic function: see plot.
x = "dti"
Returns a warning.
x = "dtiData"
gradient can be used to specify a specific data cube associated with the index of a gradient direction. For objects of class "dtiData" images are produces that are scaled by the maximal observed image value. This guarantees that subsequently produced images are on a comparable grey scale. The resulting image of class "adimpro" from package adimpro is returned.
x = "dtiIndices"
Color coded anisotropy maps are produced depending on the specification in method. method==1, method==2, method==4 and method==5 specify three different color schemes for directional FA-maps. method==3 specifies visualization of dtiIndices using color coded shape parameters. The resulting image of class "adimpro" from package adimpro is returned.
x = "dtiTensor"
The tensor itself, fractional anisotropy (FA), mean diffusivity (MD) and a color coded anisotropy map are provided. NULL is returned.

Author(s)

Karsten Tabelow tabelow@wias-berlin.de
J"org Polzehl polzehl@wias-berlin.de

See Also

dtiIndices, dtiData, dtiTensor

Examples

  ## Not run: demo(dti_art)

[Package dti version 0.6-0 Index]