dwi.smooth-methods: Smooth DWI data

Description

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.

Usage

# S4 method for 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 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)

Value

An object of class "dtiData" with smoothed diffusion weighted images.

Arguments

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 2*ncoils degrees of freedom), "Chi2" for squares of observed values (assumed to be distributed as noncentral Chi-squared with 2*ncoils 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.

Methods

signature(object) = "ANY": Returns a warning.
signature(object) = "dtiData": Smoothing of DWI data

Author