Hi, 2086--

Yes, that warning is really just a warning so that you know about the data. Always good to know what goes in to the processing, esp. if it might be problematic. Again, you have a b=5 s/mm^2 DWI for your reference-- that effectively has no diffusion info, so that is fine.

But yes, acquisitions really should have several reference volumes with b~0. I don't think that subject with motion in the only reference volume can be used; there are several other volumes with kind-of-low b-values, but I don't think it would be low enough; there is probably too much signal distortion in that subject's b0 to use it, and then those tensor fits would likely be inherently different than others in your group.

The effect of taking all those volumes-- even the very high bvalue ones-- would be to: 1) increase processing time and disk space usage (which is inconvenient, but not inherently a reason not to include them); and 2) probably include some noise along with signal in your tensor fitting from those volumes (which would provide an argument for not including them), in different parts of the brain (the noise floor gets reached differently in different parts of the brain and using different gradient directions, because the magnitude of diffusion would be different). In the AFNI nonlinear tensor fitting, we use a reweighting scheme, and likely the contribution of those volumes would be relatively low. In the TORTOISE RESTORE/iRESTORE tensor fittings, likely contributions from those volumes would also be downweighted. So, you might want to consider/discuss not include b-values greater than, say 1500 s/mm^2. It is a bit of judgment call.

--pt