Hi,

If you are creating t-maps or estimated parameters maps the two approaches should be equivalent  (if we ignore degrees of freedom ... ) since the t test will only test for the part of your seed region signal that is uncorrelated to the other parts of the model. The values  that should change are the ones of the counfounds (WM CSF movement signals). I would therefore use the approach that you have seen in the litterature so that you have a better estimation of the variance of your parameters (correct df).

cheers
JB