High-Reynolds-number experiments are conducted in the roughness sublayer of a turbulent boundary-layer developing over a cubical canopy. Stereoscopic particle image velocimetry is performed in a wall-parallel plane to evidence a high degree of spatial modulation of the small-scale turbulence around the footprint of large-scale motions, despite the suppression of the inner layer by the high roughness elements. Both Fourier and wavelets analyses show that the near-wall cycle observed in smooth-wall-bounded flows is severely disrupted by the canopy, whose wake in the roughness sublayer generates a new range of scales, closer to that of the outer-layer large-scale motions. This restricts significantly scale separation, hence a diagnostic method is developed to divide carefully and rationally the fluctuating velocity fields into large- and small-scale components. Our analysis across all turbulent kinetic energy terms sheds light on the spatial imprint of the modulation mechanism, revealing a very different signature on each velocity component. The roughness sublayer shows a preferential arrangement of the modulated scales similar to what is observed in the outer-layer of smooth-wall-bounded flows – small-scale turbulence is enhanced near the front of high momentum regions and damped at the front of low-momentum regions. More importantly, accessing spanwise correlations reveals that modulation intensifies the most along the flanks of the large-scale motions.