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Hello, I'm testing out the new s2v option in FSL 5.0.11's eddy_cuda as part of a pipeline with AutoPtx designed to extract tract size and average FA, L1, L2, L3, and MD. Adding " --mpoder=6 --slspec=slspec.txt --s2v_niter=5 --s2v_lambda=1 --s2v_interp=trilinear" drops my average FA to 58% of my initial analysis, with my average L1 increasing 48%, L2 increasing 94%, L3 increasing 135%, and MD increasing 78%. The tracts created by AutoPtx are essentially identical so it's not an issue of different regions being identified. Changing s2v_niter to 5 and s2v_lambda to 10 gave similar results. The diffusion data is 102 directions, 81 slices with a multiband factor of 3. Running dtifit shows this to be an issue for the whole brain in the attached images (range 0 to 1 for both). I was expecting my FA to increase, if anything. Any idea what's happening here? Thank you, James Kennedy Washington University ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1