Hi Finn and Rob,
Thanks for the codes.
I tried the following to register the raw T1 to the bias-corrected DTI image using flirt with 6 DOF.
flirt -in a_T1.nii -ref a_biascorrected.nii -dof 6 -out a_flirt.nii
Now that the T1 and DWI are registered, is it advisable to proceed with 5ttgen on the down sampled T1?
Cheers.