Non-local means based Rician noise filtering for diffusion tensor and kurtosis imaging in human brain and spinal cord

BACKGROUND: To investigate the effect of using a Rician nonlocal means (NLM) filter on quantification of diffusion tensor (DT)- and diffusion kurtosis (DK)-derived metrics in various anatomical regions of the human brain and the spinal cord, when combined with a constrained linear least squares (CLLS) approach. METHODS: Prospective brain data from 9 healthy subjects and retrospective spinal cord data from 5 healthy subjects from a 3 T MRI scanner were included in the study. Prior to tensor estimation, registered diffusion weighted images were denoised by an optimized blockwise NLM filter with CLLS. Mean kurtosis (MK), radial kurtosis (RK), axial kurtosis (AK), mean diffusivity (MD), radial diffusivity (RD), axial diffusivity (AD) and fractional anisotropy (FA), were determined in anatomical structures of the brain and the spinal cord. DTI and DKI metrics, signal-to-noise ratio (SNR) and Chi-square values were quantified in distinct anatomical regions for all subjects, with and without Rician denoising. RESULTS: The averaged SNR significantly increased with Rician denoising by a factor of 2 while the averaged Chi-square values significantly decreased up to 61% in the brain and up to 43% in the spinal cord after Rician NLM filtering. In the brain, the mean MK varied from 0.70 (putamen) to 1.27 (internal capsule) while AK and RK varied from 0.58 (corpus callosum) to 0.92 (cingulum) and from 0.70 (putamen) to 1.98 (corpus callosum), respectively. In the spinal cord, FA varied from 0.78 in lateral column to 0.81 in dorsal column while MD varied from 0.91 × 10(−3) mm(2)/s (lateral) to 0.93 × 10(−3) mm(2)/s (dorsal). RD varied from 0.34 × 10(−3) mm(2)/s (dorsal) to 0.38 × 10(−3) mm(2)/s (lateral) and AD varied from 1.96 × 10(−3) mm(2)/s (lateral) to 2.11 × 10(−3) mm(2)/s (dorsal). CONCLUSIONS: Our results show a Rician denoising NLM filter incorporated with CLLS significantly increases SNR and reduces estimation errors of DT- and KT-derived metrics, providing the reliable metrics estimation with adequate SNR levels.