Significance We use functional MRI to investigate the cortical effects on V1, V2, V3, hV4, and VO-1 when humans’ eyes have adapted to low-light vision. We show that populations of neurons with receptive fields interacting with the central rod scotoma are silenced because of lack of stimulation, shift their locations ectopically, and/or scale their sizes in some maps because of partial stimulation when the receptive fields overlap with the rod scotoma. These same effects have been cited as hallmarks of long-term reorganization, but our results show that these effects can be the result of the normal short-term adaptation of the visual system. In contrast, we observe no cortical differences between general rod and cone input other than rod scotoma effects. , Are silencing, ectopic shifts, and receptive field (RF) scaling in cortical scotoma projection zones (SPZs) the result of long-term reorganization (plasticity) or short-term adaptation? Electrophysiological studies of SPZs after retinal lesions in animal models remain controversial, because they are unable to conclusively answer this question because of limitations of the methodology. Here, we used functional MRI (fMRI) visual field mapping through population RF (pRF) modeling with moving bar stimuli under photopic and scotopic conditions to measure the effects of the rod scotoma in human early visual cortex. As a naturally occurring central scotoma, it has a large cortical representation, is free of traumatic lesion complications, is completely reversible, and has not reorganized under normal conditions (but can as seen in rod monochromats). We found that the pRFs overlapping the SPZ in V1, V2, V3, hV4, and VO-1 generally ( i ) reduced their blood oxygen level-dependent signal coherence and ( ii ) shifted their pRFs more eccentric but ( iii ) scaled their pRF sizes in variable ways. Thus, silencing, ectopic shifts, and pRF scaling in SPZs are not unique identifiers of cortical reorganization; rather, they can be the expected result of short-term adaptation. However, are there differences between rod and cone signals in V1, V2, V3, hV4, and VO-1? We did not find differences for all five maps in more peripheral eccentricities outside of rod scotoma influence in coherence, eccentricity representation, or pRF size. Thus, rod and cone signals seem to be processed similarly in cortex.