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Anatomic images covering the cervical spinal cord from the C1 to C6 levels and DTI, magnetization transfer/inhomogeneous magnetization transfer images at the C2/C5 levels were acquired in 19 patients with MS and 19 paired healthy controls. Anatomic images were segmented in spinal cord GM and WM, both manually and using the AMU40 atlases. MS lesions were manually delineated. MR imaging metrics were analyzed within normal-appearing and lesion regions in anterolateral and posterolateral WM and compared using Wilcoxon rank tests and z scores. The use of a multiparametric MR imaging protocol combined with an automatic template-based GM/WM segmentation approach in the current study outlined a higher sensitivity of the ihMT technique toward spinal cord pathophysiologic changes in MS compared with atrophy measurements, DTI, and conventional MT. The authors also conclude that the clinical correlations between ihMTR and functional impairment observed in patients with MS also argue for its potential clinical relevance, paving the way for future longitudinal multicentric clinical trials in MS.