dti-class {dti} | R Documentation |
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.
"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.
.Data
: "list"
, usually empty. btb
: "matrix"
, matrix of dimension c(6,ngrad)
obtained from gradient directions. ngrad
: "integer"
, number of gradients (including zero gradients). s0ind
: "integer"
, index of zero gradients within the sequence 1:ngrad
. replind
: "integer"
, index (identifier) of unique gradient directions. Used to characterize replications in the gradient design by identical indices. length is ngrad
. ddim
: "integer"
, dimension of subcube defined by xind
, yind
and zind
. ddim0
: "integer"
, dimension of original image cubes. Vector of length 3. xind
, yind
, zind
:"integer"
, index for subcube definition in x-, y- and z-direction. voxelext
: "numeric"
, voxel extensions in x-, y- and z-direction. Vector of length 3. orientation
: "integer"
, orientation of data according to AFNI convention. Vector of length 3. level
: "numeric"
, minimal valid S0-level. No evaluation will be performed for voxels with S0-values less than level
. source
: "character"
, name of the source imgage file or source directory. call
: "call"
, call that created the object.
For class "dtiData"
:
si
: "array"
, Diffusion Weighted Data. sdcoef
: "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
: "array"
, estimated tensors, dimension c(6,ddim)
.
Tensors are stored as upper diagonal matrices.th0
: "array"
, estimated intensities in S0 images, dimension ddim
sigma
: "array"
, estimated error variances if method=="linear"
, zero otherwise.scorr
: "numeric"
, estimated spatial correlations in coordinate directionsbw
: "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
: "array"
, logical indicating the voxel where the tensor was estimated.hmax
: "numeric"
, maximal bandwidth in case of adaptive smoothing, 1 otherwise.outlier
: "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
:show3d.dtiTensor
method
: "character"
, either "linear"
or "nonlinear"
or "unknown"
. Indicates the regression model used for estimating the tensors.
For class "dtiIndices"
:
fa
: "array"
, Fractional anisotropy values (FA)ga
: "array"
, Geodetic anisotropy values (GA)md
: "array"
, Mean diffusivity values (MD) andir
: "array"
, Main directions of anisotropy bary
: "array"
, Shape parameters method
: "character"
either "linear"
or "nonlinear"
or "unknown"
. Indicates the regression model used for estimating the tensors.
Methods only operate on subclasses "dtiData"
, "dtiTensor"
, and "dtiIndices"
.
signature(object = "dtiData")
: Create estimates of diffusion tensors in each voxel. signature(object = "dtiTensor")
: Create estimates of diffusion tensors indices in each voxel.
Karsten Tabelow tabelow@wias-berlin.de
J"org Polzehl polzehl@wias-berlin.de
dtiData
,
readDWIdata
,
sdpar-methods
,
dtiTensor-methods
,
dti.smooth-methods
,
dtiIndices-methods
,
plot-methods
,
print-methods
,
summary-methods
,
extract-methods