Hello FreeSurfer Developers, 

I am registering FA maps to T1 for a group of subjects with MS and in many cases the registration is poor for the anterior corpus callosum (attached), cerebellum, pons, and temporal lobe. I am using the following commands (FreeSurfer version 6.0):

bbregister \

    --dti \

    --reg diff2T1_reg.dat \

    --mov eddy_corrected_b0.nii.gz \

    --s subject_temp

mri_vol2vol \

    --mov dtifit_FA.nii.gz \

    --targ orig.mgz \

    --o FA2T1.nii.gz \

    --reg diff2T1_reg.dat

Do you have any suggestions for improving this registration? 

Thank you,
Andrew