dti-class {dti}R Documentation

Class "dti"

Description

The family of "dti" classes is used for Diffusion Weighted Imaging (DWI) data and, within the Diffusion Tensor Model (DTI), diffusion tenors and its indices.

Objects from the Class

"dti" is only a superclass, no instances should be created. However, objects can be created by calls of the form new("dti", ...). "dtiData", "dtiTensor", and "dtiIndices" can be created from their correspondingly named functions and methods.

Slots

.Data:
Object of class "list", usually empty.
btb:
Object of class "matrix", matrix of dimension c(6,ngrad) obtained from gradient directions.
ngrad:
Object of class "integer", number of gradients (including zero gradients).
s0ind:
Object of class "integer", index of zero gradients within the sequence 1:ngrad.
replind:
Object of class "integer", index (identifier) of unique gradient directions. Used to characterize replications in the gradient design by identical indices. length is ngrad.
ddim:
Object of class "integer", dimension of subcube defined by xind, yind and zind.
ddim0:
Object of class "integer", dimension of original image cubes. Vector of length 3.
xind, yind, zind:
Objects of class "integer", index for subcube definition in x-, y- and z-direction.
voxelext:
Object of class "numeric", voxel extensions in x-, y- and z-direction. Vector of length 3.
orientation:
Object of class "integer", orientation of data according to AFNI convention. Vector of length 3.
level:
Object of class "numeric", minimal valid S0-level. No evaluation will be performed for voxels with S0-values less than level.
source:
Object of class "character", name of the source imgage file or source directory.
call:
Object of class "call", call that created the object.

For class "dtiData":

si:
Object of class "array", Diffusion Weighted Data.
sdcoef:
Object of class "numeric", Parameters of the model for error standard deviation as a function of the mean. First two entries refer to intercept and slope of a linear function, third and fourth value are the endpoints of the interval of linearity. Contains rep(0,4) if not set. If the function

For class "dtiTensor":

D:
Object of class "array", estimated tensors, dimension c(6,ddim). Tensors are stored as upper diagonal matrices.
th0:
Object of class "array", estimated intensities in S0 images, dimension ddim
sigma:
Object of class "array", estimated error variances if method=="linear", zero otherwise.
scorr:
Object of class "numeric", estimated spatial correlations in coordinate directions
bw:
Object of class "numeric", bandwidth for a Gaussian kernel that approximately creates the estimated spatial correlations. Needed for adjustments of critical values in the adaptive smoothing algorithm used in function dti.smooth
mask:
Object of class "array", logical indicating the voxel where the tensor was estimated.
hmax:
Object of class "numeric", maximal bandwidth in case of adaptive smoothing, 1 otherwise.
outlier:
Object of class "numeric", index of voxel where physical constraints are not met, i.e. where the observed values in gradient images Si were larger than the corresponding S0 values. These are probably motion effects or registration errors. Values are replaced by the corresponding (mean) S0 values.
scale:
Numerical value corresponding to the 95% quantile of the maximal eigenvalues of estimated tensors within the mask. Used for scaling in function show3d.dtiTensor
method:
Object of class "character", either "linear" or "nonlinear" or "unknown". Indicates the regression model used for estimating the tensors.

For class "dtiIndices":

fa:
Object of class "array", Fractional anisotropy values (FA)
ga:
Object of class "array", Geodetic anisotropy values (GA)
md:
Object of class "array", Mean diffusivity values (MD)
andir:
Object of class "array", Main directions of anisotropy
bary:
Object of class "array", Shape parameters
method:
Object of class "character" either "linear" or "nonlinear" or "unknown". Indicates the regression model used for estimating the tensors.

Methods

Methods only operate on subclasses "dtiData", "dtiTensor", and "dtiIndices".

dti.smooth
Create estimates of diffusion tensors in each voxel using structural adaptive spatial smoothing.
dtiTensor
signature(object = "dtiData"): Create estimates of diffusion tensors in each voxel.
dtiIndices
signature(object = "dtiTensor"): Create estimates of diffusion tensors indices in each voxel.
plot
Method for Function `plot' in Package `dti'.
print
Method for Function `print' in Package `dti'.
summary
Method for Function `summary' in Package `dti'.

Author(s)

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

See Also

dtiData, readDWIdata, sdpar-methods, dtiTensor-methods, dti.smooth-methods, dtiIndices-methods, plot-methods, print-methods, summary-methods, extract-methods


[Package dti version 0.6-0 Index]