Fixel analysis on multi site, pre-post data set

So, I am working with some of my staff on a FIxel based analysis of diffusion data in a clinical sample, collected across two sites with a pre and post scan.

By way of background, I’m an fMRI researcher, less experience in diffusion, and I’m muddling my way through Fixel stuff. My RA ran a lot of the pipelines which is worse because I’m further from the data…

Firstly, I’m wondering fi anyone would like to posit a suggestion for combining multi-site data here? There are often big scanner differences in diffusion. it seems easier to model out in fMRI, and we can handle some of this post-processing. I’m a bit worried because the full sample goes into the fixel pipeline that we should try to harmonize before running MRTrixx and Fixel… but I’m not entirely clear what the best choice is. I know there is Rich harmonization but it seems to have a number of issues in actual implimentation.

Second, would really appreciate any advice on pre-post analysis. in FMRI, I would often subtract pre and post scans and run a simpler statistical set on the change maps. Not so sure this is viable in Fixel. I could set up a monster design matrix with (208) columns for participants. hoping there might be a slightly simpler approach.

THANKS TEAM!
Colin