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

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  ## S4 method for signature 'dtiData'
dwi.smooth(object, kstar, lambda=20, kappa0=NULL, ncoils=1, 
                                 sigma=NULL, level=NULL, vred=4, xind=NULL, 
                                 yind=NULL, zind=NULL, 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)

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.

Value

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

Methods

signature(object) = "ANY"

Returns a warning.

signature(object) = "dtiData"

Smoothing of DWI data

Author(s)

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

See Also

dtiData, dtiData,

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