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Hi Kavous, What are the research hypotheses? If it's about changes over timepoints, and interaction group by timepoint, then this needs the assumption of compound symmetry, which is fine for 2 timepoints, but becomes harder with 4. If you want to make that assumption, then you can use PALM, defining one exchangeablity block per subject, and permuting within-block and also whole-block (for the interactions. If you can't make the compound symmetry assumption, consider Bryan Guillaume's toolbox called SwE. It seems the most recent version is on GitHub: https://github.com/BryanGuillaume/SwE-toolbox If, however, the hypothesis is about group differences regardless of changes in time, then randomise can be used directly, with the option --permuteBlocks. This is the Example 6 of the randomise paper: http://www. sciencedirect.com/science/article/pii/S1053811914000913 Hope this helps! All the best, Anderson On 30 May 2017 at 05:05, Kavous <[log in to unmask]> wrote: > Hi FSLers, > > I'm going to analyze a longitudinal VBM between 3 groups and within 4 > time-points. > > By reading following discussions, I know that in 2 time-points analysis I > have to use all my subjects' data to make a study-specific template and > subtract pre-post data after smoothing for randomise analysis. > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;d6651f48.1008 > https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;3dc8868b.1408 > > However, my question is that is there any way to consider all 4 > time-points in a single analysis? > > Thanks, > Kavous >