Thanks, Joe.
What is the reason for using the -noreorientation option?
I actually used:
mrregister IN/wmfod_norm.mif -mask1 IN/dwi_mask_upsampled.mif ./template/wmfod_template.mif -nl_warp IN/subject2template_warp.mif IN/template2subject_warp.mif
mrtransform IN/FA.mif -warp IN/subject2template_warp.mif IN/FA.wmfod_templatespace.mif