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

In neuroconductor/dti: Analysis of Diffusion Weighted Imaging (DWI) Data

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

## S4 method for signature '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, ...)
## S4 method for signature '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,...)
## S4 method for signature '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,...)
## S4 method for signature '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, ...)
## S4 method for signature '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, ...)
## S4 method for signature '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, ...)
## S4 method for signature 'dwiFiber'
show3d(obj, add=FALSE, bgcolor="black", box=FALSE,
         title=FALSE, lwd=1, delta=0, ...)

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 "odf", "axis" and "both", with the latter superposing the estimated main directions on the estimated ODF. For "axis"(and "both") the length of the axis corresponds to the mixture weights. For dtiData-objects choices are either "data" or "adc".
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 corrsponding vertice direction of the specified polyhedron. This can lead to extremely large volumes in case of one mixture component with high excentricity. values of odfscale inbetween 1 and 3 are possible and allow to balance between volume based visualization and emphazising highly structured ODF's.
lwd	Linewidth for visualization of dtiIndices objects.
index	Eiter "FA" for fractional anisotropy index or "GA" for geodesic anisotropy index.
delta	if delta>0 Join line segments in fiber objects as long as acos of directions is smaller than delta. Reduces the size of 3D object at the cost of resolution.
...	Additional parameters passed to function rgl.par from the rgl-package.

Value

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

Methods

obj = "ANY"

Returns a warning

obj = "dtiData"

Empirical ADC's are visualized at the voxel centers. Color is determined by gradient directions, ADC values are reflected by both radial extend and transparancy. The value of maxobjects limits the size of datacube and may be increased on hardware with suitable graphics capabilities.

obj = "dtiIndices"

Objects are visualized as a collection of line segments with location given by the voxel center, orientation and color determined by the main direction of inisotropy and length corresponding to either fractional or geodesic anisotropy as specified in index.

Displayed objects are restricted to voxel with an fractional (geodesic) anisotropy larger than level.

obj = "dtiTensor"

Ellipsoids/ADC's are visualized at the voxel centers. Orientation and size correspond to the tensor values, color is determined by the main direction of anisotropy using the colorsceme specified with method. The fractional anisotropy value is coded as transparency. The value of maxobjects limits the size of datacube and may be increased on hardware with suitable graphics capabilities.

obj = "dkiTensor"

Prelimenary show3d method for diffusion kurtosis tensors.

obj = "dwiQball"

Estimated ODF/ADC's are visualized at the voxel centers. Color is determined by directions, ODF/ADC values are reflected by both radial extend and transparancy. The value of maxobjects limits the size of datacube and may be increased on hardware with suitable graphics capabilities.

obj = "dwiFiber"

Display and combine fibres generated by function tracking.

Displays can be closed using function rgl.close

Author(s)

Karsten Tabelow [e-mail]
J\"org Polzehl [e-mail]

See Also

dtiIndices-methods, dti.smooth, dtiTensor, dtiIndices

Examples

  ## Not run: demo(dti_art)

neuroconductor/dti documentation built on May 20, 2021, 4:28 p.m.