Dear Matthijs,
> The paradigm I want to study involves: rest (r) task1 task2 (control
> task)
>
> so the design is:
>
> r-t1-r-t2-r-t1-r-t1-r-t2-r
>
> The TR is 3 sec. Each epoch consists of 14 scans. The total task has
> 126 scans. I'm not sure what is meant by SOA.
This is simply Stimulus Onset Asynchrony or the interval between
successive onsets of the same trial type. The 'help' in
spm_fMRI_design explains how these define the onset of events or epochs
and how they enter into construction of regressors.
I hope this helps - Karl
spm_fMRI_design allows you to build design matrices with separable
session-specific partitions. Each partition may be the same (in which
case it is only necessary to specify it once) or different. Responses
can be either event- or epoch related, where the latter model prolonged
and possibly time-varying responses to state-related changes in
experimental conditions. Event-related response are modelled in terms
of responses to instantaneous events. Mathematically they are both
modelled by convolving a series of delta (or stick) functions,
indicating the onset of an event or epoch with a set of basis
functions. These basis functions can be very simple, like a box car,
or may model voxel-specific forms of evoked responses with a linear
combination of several basis functions (e.g. a Fourier set). Basis
functions can be used to plot estimated responses to single events or
epochs once the parameters (i.e. basis function coefficients) have
been estimated. The importance of basis functions is that they provide
a graceful transition between simple fixed response models (like the
box-car) and finite impulse response (FIR) models, where there is one
basis function for each scan following an event or epoch onset. The
nice thing about basis functions, compared to FIR models, is that data
sampling and stimulus presentation does not have to be sychronized
thereby allowing a uniform and unbiased sampling of peri-stimulus time.
spm_fMRI_design allows you to combine both event- and epoch-related
responses in the same model. You are asked to specify the number
of condition (epoch) or trial (event) types. Epoch and event-related
responses are modeled in exactly the same way by first specifying their
onsets [in terms of stimulus onset asynchronies (SOAs) or explicit onset
times] and then convolving with appropriate basis functions (short ones
for event-related models and longer ones for epoch-related respones).
Enter 0 to skip these if you only want to use regressors you have designed
outside spm_fMRI_design).
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