Background: Novel magnetic resonance (MR) imaging techniques prompted the emergence of T1-w/T2-w images or “myelin-sensitive maps (MMs)” to measure myelin in vivo. However, acquisition-related variations in MR intensities prevent meaningful quantitative comparisons between MMs. We propose an improved pipeline to standardize MMs that is applied to patients with classic trigeminal neuralgia (CTN) and trigeminal neuralgia secondary to multiple sclerosis (MSTN). Methods: 3T scanner was used to obtain T1-w and T2-w images for 17 CTN and 17 MSTN patients. Template images were obtained from ICBM152 database. MS plaques and normal-appearing white matter (NAWM) were labelled. A Gaussian curve-fit was applied to the histogram of the intensity distribution of each patient image, and transformed to match the Gaussian curve-fit of the template image. Results: MM intensities were decreased within MS plaques, compared to NAWM in MSTN patients (p<0.001) and its corresponding regions in CTN patients (p<0.001). Qualitatively, the standardized patient image and its histogram better resembled the ICBM152 template. Conclusions: MM analysis revealed reduced myelin content in MS plaques compared to corresponding regions in CTN patients and surrounding NAWM in MSTN patients. The standardized MM serves as a non-invasive, clinical tool for quantitative analyses of myelin content between different brain regions and different patients in vivo.