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Background: Quantitative Magnetization Transfer Imaging (QMTI) is often used to quantify the myelin content in multiple sclerosis (MS) lesions and normal appearing brain tissues. Also, automated classifiers such as artificial neural networks (ANNs) can significantly improve the identification and classification processes of MS clinical datasets. Objective: We classified patients with relapsing-remitting multiple sclerosis (RRMS) from healthy subjects using QMTI and T1 longitudinal relaxation time data of brain white matter and the performance of three ANN-based classifiers have been investigated. Materials and Methods: Conventional magnetic resonance imaging (MRI) and quantitative magnetization transfer scans were obtained from RRMS patients (n=30) and age-matched healthy subjects (n=30). After image pre-processing and brain tissue segmentation, QMTI parameters including magnetization transfer ratio (MTR), magnetization transfer rate (Ksat), T1 relaxation time under MT saturation pulse (T1sat) and T1 longitudinal relaxation time were calculated as parametric maps. Three ANN algorithms, including multilayer perceptron (MLP), radial basis function (RBF) and ensemble neural network based on Akaike information criterion (ENN-AIC) input features were extracted in the form of QMTI and T1 mean values. The ANNs quantitative performance is measured by the standard evaluation of confusion matrix criteria. Results: The results indicate that ENN-AIC-based classification method has achieved 90% accuracy, 92% sensitivity and 86% precision compared to other ANN classification models such as RBF and MLP. NPV, FPR and FDR values of the proposed ENN-AIC model were found to be 0.933, 0.125 and 0.133, respectively. A graphical representation of how to track actual data by the predictive values derived from each of the three algorithms, was also presented. It has been demonstrated that ENN-AIC as an effective neural network improves the quality of classification results compared to MLP and RBF. Conclusion: The efficiency and robustness of ENN classifier will greatly enhance with the use of AIC-based combination weights assignment. In addition, this research provides a new direction to classify a large amount of quantitative MRI data that can help the physician in a correct MS diagnosis.