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The paper considers the problem of motion correction in fMRI data by various methods existing in standard packages: SPM, C-PAC, BROCCOLI. The method of rigid body correction is too poor for using in real world cases, because registration of a single 3D fMRI snapshot is not instantaneous, but is performed sequentially by slices. The goals of this paper are comparison of various methods in the case of nonlinear and partial shifts and rotations of slices of fMRI records controlled artificially, and elaboration of recommendations for using these methods in different cases.