Brain Atrophy evaluation with FSL between T1 2D and T1 3D sequences

Hi everybody,

I have two MRI sequences with different acquisition protocol, the first one is a T1 MTC non volumetric sequence and the second one is a T1 TFE 3D volumetric sequence, and I want to evaluate the brain atrophy between these two MRI scan with FSL.
How can I normalize the sequences, to make them comparable, before performing the brain atrophy?

thanks to anyone who can help me