Partial damage of the primary visual cortex (V1), or damage to the white matter inputs to V1 (optic radiation), cause blindness in specific regions of the visual field. In this study, we used fMRI and quantitative pRF analysis to measure responses in patients with chronic V1 injury that resulted in blindness in a quarter of the visual field. The fMRI responses of patients and controls were generally similar, but in some patients differences from controls could be measured suggesting that there is a (limited) degree of reorganization following V1 injury. Importantly, we demonstrate that responses in spared early visual cortex are not always congruent with visual perception. Two different patterns of mismatch between responses in early visual areas and visual perception as measured by perimetry mapping were identified. In some patients, spared V1 pRF maps overlapped significantly with dense regions of the perimetric scotoma. Visual stimuli presented inside the scotoma could modulate neural activity in these voxels even though they generate no visual percept, suggesting that pRF analysis may help identify visual field locations amenable to rehabilitation. Conversely, in the remaining patients, spared V1 pRF maps failed to cover sighted locations in the perimetric map, indicating the existence of V1 bypassing pathways able to mediate useful vision. Identifying these patterns of mismatch and understanding the capacity of early visual areas to reorganize after injury is an important step which will allow us in the course of time to adopt more rational strategies for rehabilitation.