A common challenge faced by many domain experts working with time series data is how to identify and compare similar patterns. This operation is fundamental in high-level tasks, such as detecting recurring phenomena or creating clusters of similar temporal sequences. While automatic measures exist to compute time series similarity, human intervention is often required to visually inspect these automatically generated results. The visualization literature has examined similarity perception and its relation to automatic similarity measures for line charts, but has not yet considered if alternative visual representations, such as horizon graphs and colorfields, alter this perception. Motivated by how neuroscientists evaluate epileptiform patterns, we conducted two experiments that study how these three visualization techniques affect similarity perception in EEG signals. We seek to understand if the time series results returned from automatic similarity measures are perceived in a similar manner, irrespective of the visualization technique; and if what people perceive as similar with each visualization aligns with different automatic measures and their similarity constraints. Our findings indicate that horizon graphs align with similarity measures that allow local variations in temporal position or speed (i.e., dynamic time warping) more than the two other techniques. On the other hand, horizon graphs do not align with measures that are insensitive to amplitude and y-offset scaling (i.e., measures based on z-normalization), but the inverse seems to be the case for line charts and colorfields. Overall, our work indicates that the choice of visualization affects what temporal patterns we consider as similar, i.e., the notion of similarity in time series is not visualization independent.