Dear Vincent,
> the design matrices are exactly equivalent
Did you look at decimal places as well? Maybe the design matrices are just similar, not identical?
Not sure whether this is of any help, but could it be related to different settings for microtime onset/mircotime resolution? With the default setting 16 time bins a TR are calculated, and the 8th is chosen for the model, with the others being discarded. If you choose another time bin outside of SPM the time courses will differ to some extent.
Best,
Helmut
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