Thank you both for your replies. I will try the registration following your suggestions. If I
have a 2mm*2mm*2mm DWI data, would including a 2 voxel border around the lesion in
addition to the lesion mask itself be a good choice? Also, could you suggest how to invert
the lesion mask so that the in-lesion voxels have a value of 0 whereas the rest of the brain
has a value of 1? Thank you.