I had seen your post on this on the FSL list a couple weeks ago and Mark Jenkinson's response. I think he is likely right on this.
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www.jiscmail.ac.uk]
I'm not really familiar with the TBSS processing pipeline, but I don't think you will be looking at clustering of FA values, but instead at means and std. deviations over different areas. So AlphaSim would not be appropriate. I don't think we have a tool to do the permutation (bootstrapping) testing he mentioned. You could consider using just a t-test or an ANOVA (possibly over voxels using 3dttest and 3dANOVA).