Dear Susanne,
> My acquisition time for 35 slices was 4s and the interscan interval (TR) amounted to
> 14s. The auditory stimulation was moved within this 14s-time frame, which varied the
> delay between the end of the stimulation and the onset of the MR acquisition (2-8s) and
> therefore also the delay between the MR acquisition and the next auditory stimulation.
> This was done to get some information about the timing of brain activity.
Okay, that's fine.
> I now have problems with the design matrix. In the archives it said that I should use TA as
> TR (what makes sense), not to convolve with the hrf but 'use a FIR model with only a single bin
> and a basis set that is as long as your TR'. How do I manage to have only one bin?
> And isn't it possible to use the HRF but account for the delay between stimulation and the scanning
> as well as for the in-built physiological delay in the HRF by specifying my model in seconds
> and to predate my onsets so that my scan actually more or less starts at the peak of the HRF?
I'm doing my auditory studies with a deviant of the sparse sampling, but the logic is the same. I haven't used the FIR thing for a while, so, I'm not quite sure, how to setup this, but I remeber that it asks you for the number of bins ( I think, it's called 'order'). Anyway, I don't think that this would help in your case, since you have this jitter in between, which is difficult to account for in a FIR model. So, I would recommend to use a 'classical' design, i.e. TR = 14s, hrf, and precise onsets. 'Precise onsets' means that you should give the correct time of the stimulus onset, between the two scans. In your case, it might be wise to change the default 'number of bins/TR' to a number, which fits better to your real TR (e.g. 14 or 28). The latter one is to be used with caution, since it could cause some problems. You can find this option under the defaults section 'Statistics - fMRI'. The 'Sample bin' should be '1'.
Good luck,
Karsten
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Karsten Specht, PhD
Department of Biological and Medical Psychology
& National Competence Centre for functional MRI
University of Bergen
Jonas Lies vei 91
5009 Bergen
Norway
Tel.: +47-555-86279
Fax: +47-555-89872
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http://fmri.uib.no/
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