hello Bianca,

once you have a mask of your region of interest (the voxels where you have a group difference, if I got it exactly), you can simply use fslmeants and feed the skeletonized version of the FA/MD (or whatever else) volumes - I mean the 4D file with all the subjects, of course.
fslmeants will produce a text file where for each entry you have the mean value inside your region of interest.

all the best,
leonardo