Neonatal parcellation

Hi. I need to register an atlas with relative parcellation to a 3dT1 neonatal brain image in order to then extract DKI and DTI metrics over WM tracts. Registration using flirt and fnirt should be ok. My question now is which is the best way to calculate metrics over ROIs, that is extracting DKI and DTI maps just in the 122 tracts included in this JHU neonatal atlas.
Thanks Rosella