Signal hyper-intensities within brain regions have been attributed to the deposition of gadolinium following repeat administrations of MR contrast agents. These have been mainly investigated retrospectively, but acquisition parameters may have varied. We investigated the impact of altering imaging parameters when measuring phantom signal intensity ratios (SIR). By changing parameters from a baseline, it was established that the application of filters, number of coil receiver channels, and changes to TR and TE resulted in percentage signal fluctuations of similar magnitude to hyper-intensities. It is recommended that imaging parameters are standardised where possible when interpreting SIR data in longitudinal brain studies.