Dear Stephen,
I don’t wanted to say, that’s impossible to realign sessions from different days and to put them into one model in a first level design, but I was thinking that the probability of misalignment of sessions of different days will be greater than for sessions that were scanned in quick succession. Greater misalignment induces greater artefacts by applying the realignment parameters during reslicing.
I agree with the extra statistical care for repeated measures somebody needs to take on second level. But we take usually only the main effects from first level on the second level and model effects and interactions between groups conditions and treatments on the second level. The handling of contrasts is also easy in this case and there exist also a good tutorial for flexible factorial models by Jan Gläscher and Darren Gitelman.
http://www.sbirc.ed.ac.uk/cyril/downloads/Contrast_Weighting_Glascher_Gitelman_2008.pdf
kind regards,
Christoph
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