Sorry for your post going unnoticed for so long. About your question: I’m quite sure people will have different opinions on this one, but personally, I would always resize to isotropic voxels. 1.25mm, or something thereabouts, for adults should do. The benefits will be less issues / biases during template building and registration, as well as tractography potentially thereafter, and even possibly the CFE mechanism in FBA. By the time your subjects are all in template space and non-rigidly warped anyway, you’ll have samples that come from many anatomical coordinates (vs original grid) for each subject anyway, so the impact of the original anisotropic resolution of the data effectively becomes less and less as you progress beyond the upsampling step. So in summary: personally, I would certainly resample to 1.25mm isotropic when dealing with data of e.g. 2x3x3mm voxels.