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Dear Ce, > Let's say we have two sets of scan from the same subject group obtained > from two time points and we are interested to see the structural > difference between the two time points. > > When using dartel to do the preprocessing, is it necessary or > appropriate to create templates for each scan sets respectively and then > normalise to MNI space? This post from a couple of years back is a helpful overview of longitudinal analyses using DARTEL: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;e575c4c9.1010 One additional non-SPM option for longitudinal analysis is ANTS: http://www.picsl.upenn.edu/ANTS/ which I know has had some success looking at longitudinal change (e.g. Avants et al., 2009). Hope this helps! Best regards, Jonathan Reference: Avants B, Khan A, McCluskey L, Elman L, Grossman M (2009) Longitudinal cortical atrophy in amyotrophic lateral sclerosis with frontotemporal dementia. Archives of Neurology 66:138-139. -- Dr. Jonathan Peelle Center for Cognitive Neuroscience and Department of Neurology University of Pennsylvania 3 West Gates 3400 Spruce Street Philadelphia, PA 19104 USA http://jonathanpeelle.net/