Dear Mark,
Many thanks for the clarification and the rmsdiff tool. Certainly a useful tool that escaped my attention.
In addition to quantifying the amount of motion, I also want to obtain the rotation angles of the affine transformation separately. I browsed through FSL email archives and FLIRT pages but I cannot find a better answer to this other than avscale. Since you mentioned that decomposition by avscale may not produce unique results, is it possible to command FLIRT to report rotation angles when i run it on my data? This way I can ensure that the bvecs are accurately oriented.
best regards,
Tugan
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