plot {dti}R Documentation

Visualizing of dtiIndices

Description

Generic plot function for visualization of objects of class "dtiData", "dtiIndices" and class "dtiTensor"

Usage

plot(x, y, ...)

Arguments

x object of class dtiIndices, dtiData or dtiTensor
y not used
... additional arguments such as
slice
Slice number
view
choose sagittal, coronal, or axial view here
gradient
index of data cube to chose. (for class dtiData) only. Defaults to the first S0 image.
method
method==1 and method==2 specify two different color schemes for directional FA-maps. method==3 specifies visualization of dtiIndices using color coded bary coordinates. (for class dtiIndices only)
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)
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).
settings for function\code{par} (for class \code{dtiTensor} only) settings for function\code{show.image} (for class \code{dtiData} and \code{dtiIndices} only) xind{If provided restrict display to indices specified in xind for x-direction.} yind{If provided restrict display to indices specified in xind for y-direction.} zind{If provided restrict display to indices specified in xind for z-direction.}

Details

This function allows to select a slide (2D) by arguments slice and view. For objects of class "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 is returned.

For objects of class "dtiTensor" the tensor itself, fractional anisotropy (FA), mean diffusivity (MD) and a color coded anisotropy map are provided. NULL is returned.

For objects of class "dtiIndices" color coded anisotropy maps are produced depending on the specification in method. The resulting image is returned.

Value

an image of class adimpro for objects of class "dtiData" or "dtiIndices", invisible(NULL) otherwise.

Author(s)

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

References

K. Tabelow, J. Polzehl, H.U. Voss, and V. Spokoiny. Diffusion Tensor Imaging: Structural adaptive smoothing, NeuroImage 39(4), 1763-1773 (2008).

http://www.wias-berlin.de/projects/matheon_a3/

See Also

dtiIndices, dtiData, dtiTensor

Examples

## Not run: demo(dti_art)

[Package dti version 0.5-4 Index]