simVOLfmri: Simulate 3D or 4D fMRI data

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

Description

Simulates a 3D or 4D fMRI dataset for the specified design and with activation in the specified regions.

Usage

simVOLfmri(design = list(), image = list(), base=0, dim, nscan = NULL,
	TR = NULL, SNR=NULL, noise = c("none", "white", "temporal", 
	"spatial", "low-frequency", "physiological", "task-related", 
	"mixture"), type = c("gaussian", "rician"), 
	spat = c("corr", "gaussRF", "gammaRF"), weights, verbose = TRUE, 
	rho.temp = 0.2, rho.spat = 0.75, freq.low = 128, 
	freq.heart = 1.17, freq.resp = 0.2, FWHM = 4, gamma.shape = 6, 
	gamma.rate = 1, vee=1, template)

Arguments

design	List generated by simprepTemporal specifying the design. If not specified, noise images are generated.
image	List generated by simprepSpatial specifying the activated regions. If not specified, noise images are generated
base	Baseline of the data. Should be a single number or an array with the same dimensions as in dim.
dim	Dimensions of the image space.
nscan	Number of scans for noise images.
TR	Repetition time for noise images.
SNR	Signal-to-noise ratio.
noise	Type of noise, default is white.
type	If noise==white or noise==mixture, the type of system noise (default is gaussian).
spat	If noise==spatial or noise==mixture, the spatial correlation structure (default is corr).
weights	If noise==mixture, weights vector of six elements.
verbose	Logical indicating if warning should be printed.
rho.temp	If noise==temporal or noise==mixture, value of autocorrelation coefficients. The length of the vector indicates the order of the autoregressive model.
rho.spat	If noise==spatial or noise==mixture, and spat==corr, value of the correlation coefficient.
freq.low	If noise==low-frequency or noise==mixture, frequency of the low-frequency drift in seconds.
freq.heart	If noise==physiological or noise==mixture, frequency of heart rate in Hz.
freq.resp	If noise==physiological or noise==mixture, frequency of respiratory rate in Hz.
FWHM	If noise==spatial or noise==mixture, and spat==gaussRF or spat==gammaRF, value of the FWHM of the Gaussian kernel.
gamma.shape	If noise==spatial or noise==mixture, and spat==gammaRF, value of the shape parameter of the gamma distribution.
gamma.rate	If noise==spatial or noise==mixture, and spat==gammaRF, value of the rate parameter of the gamma distribution.
vee	If type==rician, non-centrality parameter of the rician distribution.
template	An array representing the anatomical structure or mask with dimensions equal to dim.

Value

A 3D or 4D array specifying the values for each voxel in the data.

Author(s)

M. Welvaert

See Also

simTSfmri, simprepTemporal, simprepSpatial

Examples

design <- simprepTemporal(totaltime=200, onsets=seq(1,200,40), 
	durations=20, TR=2, effectsize=1, hrf="double-gamma")
region <- simprepSpatial(regions=2, coord=list(c(32,15),c(57,45)), 
	radius=c(10,7), form="sphere", fading=TRUE)
out <- simVOLfmri(design=design, image=region, dim=c(64,64), 
	SNR=1, noise="none")
## Not run: plot(out[32,15,], type="l")
## Not run: library(lattice)
library(gplots)
levelplot(out[,,10],scales=list(tck=0), 
	col.regions=colorpanel(50,high="white",low="black"))
## End(Not run)

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