Dear Freesurfer community:

I have some (perhaps silly, but I think fundamental) questions about contrasts in functional analyses:


1. When wanting to see what regions are activated by exposure to a certain stimulus (blocked-design), what is the exact stats that is happening voxel-wise:

(i) correlation between the time series of the HRF-convoluted BOLD and that of the behavioural stimulus that was used, or
(ii) t-test between the BOLD signal during the stimulus and the BOLD signal during a resting baseline

If ii) is the answer, then is "baseline" taken as an average of all non-stimulus (rest) periods in the scan, i.e. the "zero" periods in the block-design boxcar diagram?



2. When wanting, on the other hand, to see what regions are active in condition A but not in condition B (so a comparison this time), is it the case that i) is no longer a choice and a t-test always has to be used between condition A and condition B? If so, is the stimulus-vs-baseline situation from the previous question just a special case of this, where condition B = (passive) baseline?



3. Is it the case that a contrast probing the difference between two groups is using independent samples t-tests, whereas one probing the within-subject difference between two time-points is using paired-samples t-tests?


Thank you for your help :-)

--Francesco