The application of a three-dimensional magnetization transfer (MT) sequence and B-spline active surface segmentation method to produce MT histograms of the cervical spinal cord in a pilot study of controls and multiple sclerosis (MS) patients is presented. Subjects' cervical spinal cords were imaged with (a) a volume-acquired inversion-prepared fast spoiled gradient echo sequence and (b) a volume-acquired noninversion-prepared fast spoiled gradient echo MT sequence. The images were segmented using the B spline active surface technique and MT histograms were produced from the MT images. The method was sensitive enough to detect differences between seven MS patients and 10 controls in mean MT ratio (42.4 pu versus 44.0 pu, p = 0.03) and peak location (45.2 versus 46.8, p = 0.03). The spinal cord volumes obtained from the two sequences were associated with each other (parameter estimate 0.972, 95% confidence intervals 0.742, 1.202, p < 0.001).