Hi I think this strategy is valid for both morphometry and spatial processing of fMRI data.
I recently came across this project that does exactly that: preparing mp2rage for freesurfer, doing so by multiplying UNI by INV2 image.
Otherwise, the more “traditional” way to deal with MP2RAGE UNI data is to use the Robust background removal method introduced by O’Brien et al (2014), that you can find in different flavors:
- matlab original scripts: https://github.com/JosePMarques/MP2RAGE-related-scripts/blob/master/DemoRemoveBackgroundNoise.m
- SPM flavored: https://github.com/benoitberanger/mp2rage
- python flavored: https://github.com/khanlab/mp2rage_genUniDen/blob/master/mp2rage_genUniDen.py
You can find other options, there is at least another one cited in this thread.