Hi Ziad-

I'm going to jump in here because Mike and I are trying to get answers to the same questions. First off--congratulations on the newborn.

In answer to your questions, we're smoothing parameters. We were being conservative and smoothing at 4mm HEAT but it doesn't seem to do much, so we knocked it up to 8mm. We were also throwing around the idea of just using the old method at either 4mm or 8mm.

1. Should we be concerned with data smoothed at 4mm HEAT?
2. Is there anything wrong with using the old method?
3. How would we go about determining internodal distance?

Since we do permutation clustering, this method intrinsically takes into account the smoothing in the data so I don't think we need exact estimates of FWHM. This may affect the answers to the above questions.

Thanks.

Anthony