Converging evidence conclusively demonstrates the robust relationship between anatomical landmarks and underlying functional organization in primary cortical regions. In consequence, a precise alignment across subjects of such specific individual landmarks should improve the overlap of the corresponding functional areas and thus the detection of active clusters at the group level. In an effort to define a dedicated processing pipeline for a fine non-invasive exploration of the motor cortex in human, we evaluated four recent non-linear registration methods based on anatomical and functional indexes. We used high-resolution functional MRI data to finely reveal the impact of the registration on the cortical assignment of the detected clusters. Our results first demonstrate that the quality of registration strongly affects the statistical significance and the assignment of activated clusters to specific anatomical regions, here in the primary motor area. Our results also illustrate the bias induced by the chosen reference template on the detected clusters. The analysis of the Jacobian of the deformation field informs us about how each method deforms the anatomical structures and functional maps. The methodology we propose, combining high resolution fMRI and non-linear registration method, allows a robust non-invasive exploration of the motor cortex.