Is it possible to flip the dwi images beforehand?
mirroring your images (after FOD calculation seems handiest to me, as you don’t have to adjust your bvecs) will be quite feasible).
Well, you still need to flip the FODs in that case. If your diffusion gradient table is embedded within the image header, then
mrtransform will deal with the gradient table flipping automatically.
If you want to make a comparison of all affected patients, the anatomical variation in your dataset might dominate your result.
One would expect in this instance that the variation in stroke location will simply result in a diffuse effect of small magnitude that won’t reach statistical significance. So I maybe wouldn’t say “dominate” the result, given FWE control will still be guaranteed.
What I would however suggest @Stephanie is carefully considering exactly what it is that you are testing. I.e. Does one expect to see an effect in hemispheres affected by stroke that is independent of the infarct location? Or further: Are you looking for a group comparison effect that cannot be explained be the locations of the infarcts (i.e. essentially “regressing out” infarct loading)? For the latter there’s the potential to utilise some of the upcoming statistical analysis goodies, if ti would make the numerical testing more faithful to your actual scientific hypothesis.