In diffusion weighted imaging (DWI), multiple acquisitions are acquired and averaged to attain a reasonable SNR level, especially for high spatial resolution or high b-value imaging. However, bulk or involuntary physiological motion during diffusion-sensitizing gradients alters the k-space, creating unpredictable global and/or local phases across multiple acquisitions. Therefore, direct complex averaging of these multiple acquisitions is prohibited. Here, we propose a reconstruction scheme based on modified anisotropic diffusion filtering, which starts with complex-valued acquisitions and corrects the phase issues while improving the SNR. The proposed reconstruction is demonstrated with in vivo DWI of the cervical spinal cord at 1.5T.