I think this has been covered in the forums before but I have not found a clear answer. What is the recommended way to combine/average fmri runs within subjects (following first-level analysis)? For example, if for each subject we have 2 fmri runs should we use the method outlined in one analysis/one model:
or should we have one separate model/analysis for each subject?
I have tried both and get simlar results but the zstats from the latter are noisier particularly on the edges of the zstats images. So this suggests that the two are not doing exactly the same computations and therefore are not answering the averaging question in exactly the same way?