plot-methods: Methods for Function 'plot' in Package 'dti' In dti: Analysis of Diffusion Weighted Imaging (DWI) Data

Description

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

Usage

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19``` ```## 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", 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), ...) ## S4 method for signature '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), ...) ## S4 method for signature '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), ...) ## S4 method for signature 'dwiFiber' plot(x, y, ...) ## S4 method for signature '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="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(s)

Karsten Tabelow [email protected]
J\"org Polzehl [email protected]

`dtiIndices`, `dtiData`, `dtiTensor` `dwiMixtensor`

Examples

 `1` ``` ## Not run: demo(dti_art) ```

Example output

```Loading required package: awsMethods

Use the function setCores() to change the number of CPU cores.

sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
Reading RAW images requires to install dcraw, see

http://cybercom.net/~dcoffin/dcraw/ for LINUX and http://www.insflug.org/raw/
for MAC OS and Windows

Warning messages:
1: In fun(libname, pkgname) : could not determine path to Imagemagick

please set the correct path manually using

'Sys.setenv(ImageMagick='path2imagemagick')'
2: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
3: 'rgl_init' failed, running with rgl.useNULL = TRUE