| plot-methods {dti} | R Documentation |
Visualization of objects of class "dtiData", "dtiIndices" and class "dtiTensor"
## 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), ...)
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 |
plot. 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. 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.NULL is returned.
Karsten Tabelow tabelow@wias-berlin.de
J"org Polzehl polzehl@wias-berlin.de
dtiIndices,
dtiData,
dtiTensor
## Not run: demo(dti_art)