plot-methods: Methods for Function `plot' in Package `dti'

Description

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

Usage

# S4 method for dtiData
plot(x, y, slice=1, gradient=NULL, view= "axial", show=TRUE,
   density=FALSE, xind=NULL, yind=NULL, zind=NULL, mar=par("mar"), mgp=par("mgp"), ...)
# S4 method for dtiTensor
plot(x, y, slice=1, view="axial", quant=0, minfa=NULL, contrast.enh=1,
    what="fa", qrange=c(.01,.99), xind=NULL, yind=NULL, zind=NULL,
    mar=par("mar"), mgp=par("mgp"), ...)
# S4 method for dwiMixtensor
plot(x, y, slice=1, view="axial", what="fa", minfa=NULL,
     identify=FALSE, xind=NULL, yind=NULL, zind=NULL, mar=par("mar"), mgp=par("mgp"), ...)
# S4 method for dtiIndices
plot(x, y, slice=1, view= "axial", method=1, quant=0, minfa=NULL,
   show=TRUE, identify=FALSE, density=FALSE, contrast.enh=1, what="fa",
   xind=NULL, yind=NULL, zind=NULL, mar=par("mar"), mgp=par("mgp"), ...)
# S4 method for dwiFiber
plot(x, y, ...)
# S4 method for dkiIndices
plot(x, y, slice=1, what=c("md", "fa", "mk", "mk2",
     "k1", "k2", "k3", "kaxial", "kradial", "fak"), xind=NULL, yind=NULL,
     mar=par("mar"), mgp=par("mgp"), ...)

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(minfa) specify minfa as corresponding quantile of the fractal anisotropy (FA) index.
minfa: Display only information for voxel with (G)FA>minfa
show: Visualize information in a graphics device (for classes "dtiData" and "dtiIndices" only).
identify: Enable identification of coordinates by mouse actions, logical with default FALSE. Uses function identify. (for classes "dtiIndices" and "dwiMixtensor" 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: In case of class "dtiIndices" what="ga" uses geodesic anisotropy (GA) in contrast to what="fa" for fractional anisotropy (FA). For class "dwiMixtensor" what="fa" for FA and what="order" for the number of mixture components may be chosen.
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 = "dwi": 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==6 uses colored FA maps based on scheme developed at Uni Muenster (M. Deppe, Germany). method==3 specifies visualization of dtiIndices using color coded shape parameters. If identify==FALSE the resulting image of class "adimpro" from package adimpro, otherwise a matrix with coordinates of identified voxel is returned.
x = "dtiTensor": The tensor itself, fractional anisotropy (FA), mean diffusivity (MD) and a color coded anisotropy map are provided. NULL is returned.
x = "dwiMixtensor": Depending of what images of FA (what="fa"), number of mixture components (what="order"), effective order (what="eorder") or maximum eigenvalues (what="ev"). is returned.
x = "dwiFiber": Creates a density plot of fiber lengths. NULL is returned.
x = "dkiIndices": Prelimanary function to plot a slice of diffusion kurtosis indices: Mean Kurtosis what="mk" or what="mk2", mean diffusivity what="md", fractional anisotropy what="fa".

Author

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

Examples

Run this code

  if (FALSE) demo(dti_art)

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Description

Usage

Arguments

Methods

Author

See Also

Examples