Intra-subject Inter-Day registration is slightly tricky. We wrote a document describing the procedures: [
afni.nimh.nih.gov] . I
think Ziad Saad also wrote something about this, but he's out of town the rest of this week.
Once you have done inter-day registration
before 3dTcat, you can then deal with 3dDeconvolve and normalization. There is an effect that occurs when the scanner is adjusted to each person -- this may affect the images, since the adjustments will not be the same from day-to-day. The effect shows up as a large difference in the baseline levels of the images. If you see this (e.g., the images on day 1 have numbers of about 400 and on day 2 have numbers of about 600), then you have to normalize each day separately prior to 3dTcat and 3dDeconvolve. If this effect is small-to-negligible, then you can proceed normally.
zorkon the magnificent
