fmri (version 1.7-2)

fmri.stimulus: Linear Model for FMRI Data

Description

Create the expected BOLD response for a given task indicator function.

Usage

fmri.stimulus(scans = 1, onsets = c(1), durations = c(1), TR = 2,
                times = FALSE, type = c("canonical", "gamma", "boxcar", "user"),
                par = NULL, scale = 10, hrf = NULL, verbose = FALSE)

Arguments

scans

number of scans

onsets

vector of onset times (in scans)

durations

vector of duration of ON stimulus in scans or seconds (if !is.null(times))

TR

time between scans in seconds (TR)

times

onset times in seconds. If present onsets arguments is ignored.

type

One of "canonical", "gamma", "boxcar", "user"

par

Possible parameters to the HRF.

scale

Temporal undersampling factor

hrf

If type is "user" this should be a function evaluating the hemodynamic response function

verbose

Report more if TRUE

Value

Vector with dimension c(scans, 1).

Details

The functions calculates the expected BOLD response for the task indicator function given by the argument as a convolution with the hemodynamic response function.

For type is "canonical" the latter is modelled by the difference between two gamma functions as given in the reference (with the defaults for a1, a2, b1, b2, cc given therein):

$$\left(\frac{t}{d_1}\right)^{a_1} \exp \left(-\frac{t-d_1}{b_1}\right) - c \left(\frac{t}{d_2}\right)^{a_2} \exp \left(-\frac{t-d_2}{b_2}\right) $$

The parameters a1, a2, b1, b2, cc of this function can be changed through the argument par in this order.

Other choices are a simple gamma function

$$\frac{1}{k\tau_h (k-1)!} \left( \frac{t}{\tau_h} \right)^k \exp \left( - \frac{t}{\tau_h} \right)$$

or the "boxcar" stimulus, or a user defined function hrf.

The dimension of the function value is set to c(scans, 1).

If !is.null(times) durations are specified in seconds.

References

Worsley, K.J., Liao, C., Aston, J., Petre, V., Duncan, G.H., Morales, F., Evans, A.C. (2002). A general statistical analysis for fMRI data. NeuroImage, 15:1-15.

Polzehl, J. and Tabelow, K. (2007) fmri: A Package for Analyzing fmri Data, R News, 7:13-17 .

See Also

fmri.design, fmri.lm

Examples

# NOT RUN {
  # Example 1
  hrf <- fmri.stimulus(107, c(18, 48, 78), 15, 2)
  z <- fmri.design(hrf, 2)
  par(mfrow=c(2, 2))
  for (i in 1:4) plot(z[, i], type="l")

# }