Diffusion MRI based fiber orientation distribution (FOD) estimates are widely used to examine structural connectivity in the brain. For group comparison using nonlinear spatial normalization, FOD needs to be adjusted based on the estimated degree of rotation and scaling at each voxel. We compared the current method implemented in Mrtrix for spatial normalization of FODs with an image-based method. The results suggest that the method in Mrtrix is accurate for rotation but generates potential bias in FOD peak amplitude and orientation when large anisotropic scaling is present. This knowledge is important for studies to use spatially normalized FOD maps.