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I am designing an fMRI experiment whereby, for each trial, subjects need to listen to an auditory stimulus (of arbitrary duration), and subsequently give a rating for each stimulus.

I intend to compare the BOLD signal for the different conditions under which that stimulus is presented. Thus, the part (epoch) of the trial that is of interest for analyses (contrasts) is when the stimulus is presented.

My question: is there any reason (to do perhaps with MR physics or statistical analyses) whereby the duration of the epoch of interest (i.e. of the auditory stimuli) should be an integer multiple of the TR, or can this really be arbitrary?

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  • $\begingroup$ If you give an idea of what the range of epochs you are considering (rather than just describing them as arbitrary) I could tailor the answer a bit. $\endgroup$ – Bryan Krause Aug 15 at 16:46
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Maybe to add to the previous answer because I think it does not adress the core question:

I think there are two reasons you might want to jitter your stimulus onset in relation to the TR. 1) Design/shape considerations 2) psychological considerations

1) Design effect: If you are only interested in BOLD amplitude, then you might not want to jitter. This allows you to do very simple analyses without any deconvolution/hemodynamic basis functions. Because you measure the BOLD response at the same point in time, you can simply average the 1st,2nd,3rd etc. TR after stimulus onset. But if you are interested in the shape of the BOLD response, then you might miss the peak, miss the undershoot etc. Thus for an acurate estimation of the shape, you should jitter the stimulus onset. In other words, jittering gives you a higher sampling rate at the cost of less samples per sampling point (less power without assuming a BOLD shape). enter image description here

In this image you can see that on the left side, by chance (or on purpose) we sample very close to the BOLD peak - great! On the right side, we jittered the stimulus relative to the TR. We now sample the BOLD response more uniformly, but averaging is more difficult.

Note that this is related but a bit orthogonal to the event-related / blocked design decision.

2) Psychological Effect: If you always present the stimulus at integer TRs (e.g. with a TR of 2s), subjects will synchronize with your experiment and expect the stimulus. Whether this is something you want, you need to decide for yourself.

More information can be found here: http://mindhive.mit.edu/book/export/html/74

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  • $\begingroup$ That's really helpful, thank you!! $\endgroup$ – z8080 Sep 19 at 21:32
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The biology underlying the BOLD response is much slower than typical TRs, so I would say on one hand it doesn't really matter because the TR interval is not the time scale that matters. On the other hand, if you are presenting stimuli of duration where the TR matters, those stimuli are occurring too quickly to be resolved separately using fMRI. You may be able to solve this problem by averaging over many stimulus presentations with orders in different combinations, but that may increase your scan time more than having space between epochs and requires independence assumptions that are likely to be inappropriate.

In summary, look at the structure of some auditory fMRI tasks and see how they are organized before designing your own.

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  • $\begingroup$ Makes sense, thank you Bryan. $\endgroup$ – z8080 Aug 16 at 9:15

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