Hey @jingleil,
Yes, just for the record: I can fully support @mblesac’s answer here: mtnormalise is much more reliable. Technically you need at least 2 tissues in the model for this to become at least sensible, but in practice I’ve noticed 3 is highly preferable. For lower b-values (or for extremely high b-values actually too) for example, using 2 tissues (WM and CSF, that is) with mtnormalise introduces a few concerns. For reference, I’ve mentioned some of this as well over here and over here on the forum. To avoid these concerns, always use 3 tissues; either using MSMT-CSD or SS3T-CSD, depending on your data and what metric you wish to extract.
Cheers,
Thijs