Brain MR image intensities do not have a fixed tissue-specific value. Especially in longitudinal studies, where a subjects’ anatomy might change, pathology can arise, scanner software and hardware may be replaced, the resulting image intensities can differ widely. This thwarts subsequent post-processing or image analysis. Various image intensity normalization techniques exist, but are often evaluated on healthy subjects. In this work, we evaluate six normalization techniques on 25 image-pairs (five year interval) of subjects with brain pathology. Traditional methods (e.g. Gaussian and Z-Score) are clearly affected by the presence of pathology and perform less than more recent techniques.