dti (version 1.2-0.1)

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

Description

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

Usage

## S3 method for class '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), ...)
## S3 method for class '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=c(2,2,2,.2), mgp=c(2,1,0), ...)
## S3 method for class 'dwiMixtensor':
plot(x, y, slice=1, view="axial", what="fa", minfa=NULL,  
     identify=FALSE, xind=NULL, yind=NULL, zind=NULL, mar=c(2,2,2,.2),mgp=c(2,1,0), ...)
## S3 method for class '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=c(3,3,3,.3), mgp=c(2,1,0), ...)
## S3 method for class 'dwiFiber':
plot(x, y, \dots)
## S3 method for class 'dkiIndices':
plot(x, y, slice=1, what=c("md", "fa", "mk", "mk2"), ...)

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="ord

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

See Also

dtiIndices, dtiData, dtiTensor dwiMixtensor

Examples

demo(dti_art)