spatialnoise: Generate spatially correlated noise

In NeuroStat/neuRosim: Functions to Generate fMRI Data Including Activated Data, Noise Data and Resting State Data

Description

Generates a spatially correlated noise dataset with specified dimensions and standard deviation.

Usage

spatialnoise(dim, sigma, nscan, method = c("corr", "gammaRF", "gaussRF"), 
	type=c("gaussian","rician"), rho = 0.75, FWHM = 4, gamma.shape = 6, 
	gamma.rate = 1, vee=1, template, verbose = TRUE)

Arguments

dim	A vector specifying the dimensions of the image.
sigma	The standard deviation of the noise.
nscan	The number of scans in the dataset.
method	Method specifying the type of spatial correlation. Default is "corr".
type	Type of distribution if method=="corr". Default is "gaussian"
rho	If method=="corr", the value of the autocorrelation coefficient.
FWHM	If method=="gammaRF" or method=="gaussRF", the full-width-half-maximum of the Gaussian kernel.
gamma.shape	If method=="gammaRF", the shape parameter of the Gamma distribution.
gamma.rate	If method=="gammaRF", the shape parameter of the Gamma distribution.
vee	If method=="corr" and type=="rician", the non-centrality parameter of the rician distribution.
template	An array representing the anatomical structure or mask with dimensions equal to dim.
verbose	Logical indicating if warnings should be printed.

Details

The function generates spatially correlated noise. When method=="corr", AR(1) voxelwise correlations are introduced. If method=="gaussRF" of method=="gammaRF", respectively a Gaussian Random Field or a Gamma Random Field is created. The result is a noise array with specified dimensions and desired standard deviation. The generation of the random fields is based on the function Sim.3D.GRF from J.L. Marchini in the package AnalyzeFMRI.

Value

An array containing the noise with dimensions specified in dim and nscan.

Author(s)

J. Durnez, B. Moerkerke, M. Welvaert

See Also

temporalnoise, lowfreqdrift, physnoise, tasknoise, systemnoise, Sim.3D.GRF

Examples

d <- c(10,10,10)
sigma <- 5
nscan <- 100
rhospat <- 0.7
out <- spatialnoise(d, sigma, nscan, method="corr", rho=rhospat, verbose=FALSE)

NeuroStat/neuRosim documentation built on Sept. 14, 2019, 10:37 a.m.