Neglect and hemianopia are two neuropsychological syndromes that are associated with reduced awareness for visual signals in patients' contralesional hemifield. They offer the unique possibility to dissociate the contributions of retino-geniculate and retino-colliculo circuitries in visual perception. Yet, insights from patient fMRI studies are limited by heterogeneity in lesion location and extent, long-term functional reorganization and behavioural compensation after stroke. Transcranial magnetic stimulation (TMS) has therefore been proposed as a complementary method to investigate the effect of transient perturbations on functional brain organization. This concurrent TMS-fMRI study applied TMS perturbation to occipital and parietal cortices with the aim to 'mimick' neglect and hemianopia. Based on the challenges and interpretational limitations of our own study we aim to provide tutorial guidance on how future studies should compare TMS to primary sensory and association areas that are governed by distinct computational principles, neural dynamics and functional architecture.