dwi.smooth-methods: Smooth DWI data
In neuroconductor/dti: Analysis of Diffusion Weighted Imaging (DWI) Data

Description Usage Arguments Value Methods Author(s) See Also

Adaptive smoothing of DWI data. Smoothing is performed both in space and on the sphere (e.g. between images obtained for different gradient directions) employing a natural geometrical distance ( in SE(3)). Structural adaptation is used in space only. Method dwi.smooth refers to the original POAS approach for single shell data. Method dwi.smooth.ms implements an improved method that is applicable for both single and multi-shell data.

  ## S4 method for signature 'dtiData'
dwi.smooth(object, kstar, lambda=20, kappa0=NULL, mask=NULL, ncoils=1,
                                 sigma=NULL, level=NULL, vred=4, verbose=FALSE, dist=1, 
                                 model=c("Gapprox","Gapprox2","Chi","Chi2"))
  ## S4 method for signature 'dtiData'
dwi.smooth.ms(object, kstar, lambda=12, kappa0=.5, ncoils=1,
                                    sigma=NULL, ws0=1, level=NULL, mask = NULL, xind=NULL,
                                    yind=NULL, zind=NULL, verbose=FALSE,
                                    usemaxni=TRUE, memrelease = TRUE)

`object`	Object of class `"dtiData"`
`kstar`	Number of steps in structural adaptation
`lambda`	Scale parameter in adaptation
`kappa0`	determines amount of smoothing on the sphere. Larger values correspond to stronger smoothing on the sphere. If `kappa0=NULL` a value is that corresponds to a variace reduction with factor `vred` on the sphere.
`ncoils`	Number of coils in MR system
`sigma`	Error standard deviation. Assumed to be known and homogeneous in the current implementation. A reasonable estimate may be defined as the modal value of standard deviations obtained using method `getsdofsb`.
`level`	Threshold for image intensities when setting mask.
`mask`	Binary 3D image defining a mask
`vred`	Used if `kappa0=NULL` to specify the variance reduction on the sphere when suggesting a value of kappa0
`xind`	index for x-coordinate
`yind`	index for y-coordinate
`zind`	index for z-coordinate
`verbose`	If `verbose=TRUE` additional reports are given.
`dist`	Distance in SE3. Reasonable values are 1 (default, see Becker et.al. 2012), 2 ( a slight modification of 1: with k6^2 instead of abs(k6)) and 3 (using a 'naive' distance on the sphere)
`model`	Determines which quantities are smoothed. Possible values are `"Chi"` for observed values (assumed to be distributed as noncentral Chi with `2ncoils` degrees of freedom), `"Chi2"` for squares of observed values (assumed to be distributed as noncentral Chi-squared with `2ncoils` degrees of freedom). `"Gapprox"` and `"Gapprox2"` use a Gaussian approximation for the noncentral Chi distribution to smooth ovserved and squared values, respectively.
`ws0`	Factor to downweight information from S0 images, defaults to `1/numer of s0 images`.
`usemaxni`	If `"usemaxni==TRUE"` a strikter penalization is used.
`memrelease`	If `"memrelease==TRUE"` try to release allocated memory whenever possible.