An important question is whether the adult visual cortex is able to reorganize in subjects with visual field defects (scotomas) as a result of retinal or cortical lesions. Functional magnetic resonance imaging (fMRI) methods provide a useful tool to study the population receptive field (pRF) properties and assess the capacity of the human visual cortex to reorganize following injury. However, these methods are prone to biases near the boundaries of the scotoma. Distinguishing pRF changes that occur as the result of true reorganization versus different test-stimulus presentation conditions is an important task that needs to be undertaken when studying the organization of visual cortex in patients with visual field deficits. The purpose of this work was to point out some of the issues involved. We measured responses in human area V5/MT+ in five healthy subjects after masking the stimulus in the left upper quadrant of the visual field (“artificial scotoma” or AS). This simulates a homonymous quadrantanopic scotoma that occurs often as result of partial V1 or optic radiation lesions. We compared responses obtained under the AS condition with simulations obtained from a linear AS model (or LAS model). We found pRF changes in hV5/MT+ under the AS condition that are significantly different than those obtained with the LAS model suggesting that the pRFs are nonlinearly affected by the truncated stimulus presented. This was signified by a shift of the pRF centers towards the border of the AS, a decrease in pRF size and an increase in pRF amplitude near the AS border. In addition, we found erroneous pRF estimates inside the area corresponding to the AS, when we used the full bar stimulus model for predicting the pRF topography when the actual stimulus presented included the AS. These biases are not the result of a trivial methodological artifact but appear to originate from asymmetric BOLD responses occurring when the stimulus moves from seeing to non-seeing locations of the visual field. We argue that these responses are not simply neural anticipatory responses but likely contain a significant hemodynamic component.