I am hoping to apply the methods to find percent signal change, as described in the ANOVA how-to (and elsewhere) to my data.

The issue is I have two days of data for each subject, and would like to register each in common space (i.e. day 1 space for each person).

If I apply the baseline correction to the raw data before I register the images, will the beta weights of the model still reflect % signal change? I am concerned that the interpolation will throw everything out of whack.

Do you recommend applying the baseline correction after I move the data (I'd rather not, as each day involves 9 runs, and it seems cumbersome to have to register each run separately, apply the normalization to each run, and then concatenate runs.)

By the way, I love the new format/content of the How-tos!