Several nonrigid registration algorithms have been proposed for inter-subject alignment, used to construct statistical atlases and to identify group differences. Assessment of the accuracy of nonrigid registration algorithms is an essential and complex issue due to its intricate framework and its application-dependent behavior. We demonstrate that the diffusion MRI provides an independent means of assessing the quality of alignment achieved on the structural MRI. Diffusion tensor MRI (DT MRI) enables the comparison of the local position and orientation of regions that appear homogeneous in conventional MRI. We carried out inter-subject alignment of conventional T1-weighted MRI with three different registration algorithms. Consequently, we projected DT MRI of each subject through the same inter-subject transformation. The quality of the inter-subject alignment is assessed by estimating the consistency of the aligned DT-MRI using the Log-Euclidean framework.