Many current methods for multiple sclerosis (MS) lesion segmentation require radiologist seed points as input, but do not necessarily allow the expert to work in an intuitive or efficient way. Ironically, most methods also assume that the points are placed optimally. This paper examines how seed points can be processed with intuitive heuristics, which provide improved segmentation accuracy while facilitating quick and natural point placement. Using a large set of MRIs from an MS clinical trial, two radiologists are asked to seed the lesions while unaware that the points would be fed into a classifier, based on Parzen windows, that automatically delineates each marked lesion. To evaluate the impact of the new heuristics, an interactive region-growing method is used to provide ground truth and the Dice coefficient (DC) and Spearman’s rank correlation are used as the primary measures of agreement. A stratified analysis is performed to determine the effect on scans with low-, medium-, and high lesion loads. Compared to the unenhanced classifier, the heuristics dramatically improve the DC (+32.91 pt.) and correlation (+0.50) for the scans with low lesion loads, and also improve the DC (+14.55 pt.) and correlation (+0.15) for the scans with medium lesion loads, while having aminimal effect for the scans with high lesion loads, which are already segmented accurately by Parzen windows.With the heuristics, the DC is close to 80% and the correlation is above 0.9 for all three load categories.