dti (version 1.2-0.1)

show3d-methods: Methods for Function `show3d' in Package `dti'

Description

The function provides 3D visualization of "dtiData", "dtiTensor", "dwiQball" and "dtiIndices" objects using the "rgl"-package. Functionality of the rgl-package allows to rotate and zoom the displayed object.

Usage

## S3 method for class 'dtiData':
show3d(obj, xind=NULL, yind=NULL, zind=NULL, quant=.8, 
         scale=.4,
         bgcolor="black", add=FALSE, maxobjects=729, what=c("adc","data"), 
         minalpha=1, nn=1, normalize=FALSE, box=FALSE, title=FALSE, ...)
## S3 method for class 'dtiTensor':
show3d(obj, xind=NULL, yind=NULL, zind=NULL, method=1,
         minfa=.3, mask=NULL, fibers=FALSE, 
         maxangle = 30,level=0, quant=.8, scale=.4, bgcolor="black", add=FALSE, 
         subdivide=2, maxobjects=729, what=c("tensor","adc","odf"), odfscale = 1, 
         minalpha=.25, normalize=NULL, box=FALSE, title=FALSE,...)
## S3 method for class 'dkiTensor':
show3d(obj, xind=NULL, yind=NULL, zind=NULL, method=1, 
         minfa=.3, mask=NULL, level=0, quant=.8, scale=.4, bgcolor="black", 
         add=FALSE, subdivide=2, maxobjects=729, what=c("KT", "DT"),  
         minalpha=.25, normalize=NULL, box=FALSE, title=FALSE,...)
## S3 method for class 'dtiIndices':
show3d(obj, index=c("fa","ga"), xind=NULL, yind=NULL, 
         zind=NULL, method=1, 
         minfa=0, bgcolor="black", add=FALSE, lwd=1, box=FALSE, 
         title=FALSE, ...)
## S3 method for class 'dwiMixtensor':
show3d(obj, xind=NULL, yind=NULL, zind=NULL, minfa=.3, 
         minorder = 1, mineo=1, fibers=FALSE, maxangle=30, level=0,           
         quant=.8, scale=.4, bgcolor="black", add=FALSE, 
         subdivide=3, maxobjects=729, what=c("odf","axis","both"), odfscale=1, 
         minalpha=1, lwd=3, box=FALSE, title=FALSE, ...) 
## S3 method for class 'dwiQball':
show3d(obj, xind=NULL, yind=NULL, zind=NULL, level=0, 
         quant=.8, scale=0.4, odfscale=1, bgcolor="black", add=FALSE, 
         subdivide=3, maxobjects=729, minalpha=1, box=FALSE, 
         title=FALSE, \dots)
## S3 method for class 'dwiFiber':
show3d(obj, add=FALSE, bgcolor="black", box=FALSE, 
         title=FALSE, lwd=1, \dots)

Arguments

obj

An object of class dtiData, dtiTensor, dtiIndices,dwiMixTensor or dwiQball

xind

vector of x-coordinates, defaults to whole range.

yind

vector of y-coordinates, defaults to whole range.

zind

vector of z-coordinates, defaults to whole range.

quant

Quantile of maximal radii of objects used for scaling.

scale

Scale factor for the size of objects

bgcolor

Backgroundcolor for rgl-display

add

If true information is added to the current device, otherwise a new device is opened.

maxobjects

Maximal size of data cube (in voxel) to display

minalpha

Minimum value for transparency.

nn

Number of nearest neighbors used for interpolation onto a regular polyeder.

normalize

If TRUE normalize values (project to interval (0,1) within each voxel). For tensor objects normalize=NULL specifies a default depending on the content of argument what

(normalize <- switch(what,"tensor"=FALSE,"adc"=TRUE)<

box

Logical, add a bounding box.

title

Either a character string specifying a title or a logical. If title==TRUE a default title characterizing the type of plot is generated.

method

method==1 and method==2 specify two different color schemes for directional FA-maps.

minfa

Minimal FA value for dtiTensor objects and for dwiMixtensor objects.

mask

additional mask for dtiTensor objects.

minorder

Minimal order for dwiMixtensor objects.

mineo

Minimal effective order for dwiMixtensor objects.

fibers

If TRUE show fibers starting in voxel with fa>=minfa, order>=minorder and eorder>=mineo, the last two effective for dwiMixtensor objects only.

maxangle

argument for fibertracking

level

Radius of sphere used as support for ODF visualisation

subdivide

Level of subdivisions for meshing, level 0:4 correspond to use of c(12,42,162,642,2562) vertices per tensor, respectively.

what

For dtiTensor-objects either "tensor" for visualization using ellipsoids, "adc" for Apparent Diffusion Coefficients or "odf" for the Orientation Density Function. For dwiMixtensor-objects possible specifications are

odfscale

Determines visualisation of the Orientation density function (ODF). For odfscale=3 the ODF values are rescaled such that the volume of the displayes objects is constant. odfscale=1 uses the values of the ODF as radii in the c

lwd

Linewidth for visualization of dtiIndices objects.

index

Eiter "FA" for fractional anisotropy index or "GA" for geodesic anisotropy index.

...

Additional parameters passed to function rgl.par from the rgl-package.

Value

• The function returns the number of the current rgl-device.

See Also

dtiIndices-methods, dti.smooth, dtiTensor, dtiIndices

Examples

demo(dti_art)