For reference, other considerations to be careful about (e.g. with mtnormalise and other steps in mind): FBA Single Shell - High GM FOD values
It might not really have been mentioned before as well, but also be careful what masks you give to mtnormalise if you’d run 2- or even 3-tissue CSD only in an FA>… mask. You may cut out most if not all of the areas that have contributions of the other tissue types (and more, e.g. introduce holes). That’s going to be a problem that’ll undermine mtnormalise's accuracy, potentially a lot. mtnormalise thrives upon the info of all tissue types to do its job well (it’s more complicated than that; but it’s the simplest way I can put it).