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Hi Matthew:

I'm wondering if Kevin is asking a slightly different question than you answered. I have posted the question I think he's asking in the past, and never got an answer. 

Your answer allows you to use fslmeants to get a group-level timeseries, but all that returns is the average activation for each subject, as a single value, not as a function of time. In fact at the group level, calling the output of fslmeants a "time series" is really a misnomer. 

If I'm not mistaken, what is really wanted is: can you get the average time series for the group, presumably for a given mask and condition. This would entail say, specifying: " I want to see the average time series for EV-1, across subjects, drawn out to n seconds, or n TRs." Loads of papers display this information, but I've never found a good way to get this info in FSL. 

I know that if you use fslmeants at the individual bold level, you can get time-series values that are genuinely across time. However, let's say your condition of interest is randomly intermixed with other conditions within a single bold. Then to get the average timeseries for the desired EV, you'd have to identify which TRs in each bold correspond to that EV and (I guess) average the TR values  corresponding to the desired condition.What's more, if you ran a number of such bolds for each subject, then you are averaging both within and across bolds. 

Is this a kosher strategy? More to the point, since it is such a common thing to want when publishing results, I'm surprised FSL doesn't offer a function for this.

Thanks for your help...
-Christina Fales