SmoothEst: Estimate the variance-covariance matrix of a Gaussian random...

In AnalyzeFMRI: Functions for Analysis of fMRI Datasets Stored in the ANALYZE or NIFTI Format

Description

Estimate the variance-covariance matrix of a Gaussian random field

Usage

SmoothEst(mat, mask, voxdim, method = "Forman")

Arguments

mat	3D array that is the Gaussian Random Field.
mask	3D mask array.
voxdim	Vector of length 3 containing the voxel dimensions.
method	The estimator to use. method = "Forman" (the default) uses the estimator proposed in [1]. method = "Friston" uses the estimator proposed in [2, 3], but tis can be biased when the amount of smoothing is small compared to the size of each voxel (see [1] for more details and example below)

Details

Calculates the varaince-covariance matrix using the variance covariance matrix of partial derivatives.

Value

A (3x3) diagonal matrix.

Author(s)

J. L. Marchini

References

[1] Stephen D. Forman et al. (1995) Improved assessment of significant activation in functional magnetic resonance imaging (fMRI): Use of a cluster-size threshold. Magnetic Resonance in Medicine, 33:636-647.

[2] Karl J. Friston et al. (1991) Comparing functional (PET) images: the assessment of significant change. J. Cereb. Blood Flow Metab. 11:690-699.

[3] Stefan J. Kiebel et al. (1999) Robust smoothness estimation in statistical parametric maps using standardized residuals from the general linear model. NeuroImage, 10:756-766.

Examples

###############
## EXAMPLE 1 ##
###############
## example that illustrates the bias of the Friston
## method when smoothing is small compared to voxel size
## NB. The presence of bias becomes clearer if the
##     simulations below are run about 100 times and
##     the results averaged

ksize <- 13
d <- c(64, 64, 64)
voxdim <- c(1, 1, 1)
FWHM <- 2 ## using a small value of FWHM (=2) compared to voxel size (=1)
sigma <- diag(FWHM^2, 3) / (8 * log(2))
mask <- array(1, dim = d)
num.vox <- sum(mask)

grf <- Sim.3D.GRF(d = d, voxdim = voxdim, sigma = sigma,
                  ksize = ksize, mask = mask, type = "field")$mat
               
sigma
SmoothEst(grf, mask, voxdim, method = "Friston")
SmoothEst(grf, mask, voxdim, method = "Forman") ## compared to sigma
##the Forman estimator is better (on average) than the Friston estimator

###############
## EXAMPLE 2 ##
###############
## increasing the amount of smoothing decreases the bias of the Friston estimator

ksize <- 13
d <- c(64, 64, 64)
voxdim <- c(1, 1, 1)
FWHM <- 5 ## using a large value of FWHM (=5) compared to voxel size (=1)
sigma <- diag(FWHM^2, 3) / (8 * log(2))
mask <- array(1, dim = d)
num.vox <- sum(mask)

grf <- Sim.3D.GRF(d = d, voxdim = voxdim, sigma = sigma,
                  ksize = ksize, mask = mask, type = "field")$mat

SmoothEst(grf, mask, voxdim, method = "Friston")
SmoothEst(grf, mask, voxdim, method = "Forman")                
sigma

AnalyzeFMRI documentation built on Oct. 5, 2021, 5:06 p.m.