Multi-channel acquisition is employed in MRI to decrease total imaging time. In this paper, artifact free images are calculated by utilizing the difference in spatial encoding of the MR signal from neighboring channels. The encoding functions are estimated in the presence of noise and motion. For fMRI studies, the temporal stability of the signal is essential, since neuronal activity in the brain is detected by probing subtle BOLD (blood oxygen level dependent) signal changes. To ensure artifact free noise representation a new type of weight is used. By effectively selecting and eliminating low SNR pixels, increased temporal stability is achieved. Using the parallel imaging method SENSE the proposed method is tested with in-vivo data to ensure noise suppression and demonstrate correct assignment of fMRI activation.