A method for suppressing the noise component of a measured magnetic resonance (MR) signal is disclosed. In particular, a signal-space projection operator is produced and employed to suppress the noise component from acquired MR signals that is uncorrelated with the spatial pattern of a desired NMR signal. In one embodiment, an fMRI scan is performed to acquire time course image data. The NMR data is filtered with a signal-space projection operator and reconstructed into a series of image frames. In another embodiment, the signal-space projection operator is employed to suppress lipid signal in MRS image data.