I would like to carry out a longitudinal VBM study (single group measured at two time points) but as I understand it FSL does not currently support this type of analysis - largely due (i think) to the fact that there is no consensus on how to generate a suitable template. What I can't fathom is why a template generated from all your subjects would not be suitable? If I had a unpaired design I could create an unbiased template by using an equal number of subjects from each group and that woud be fine. In a paired design, if I use all my data don't I again produce an unbiased template? I could then normalize all my data to this template and run a paired samples t-test? What am I missing? Cheers.