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.