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Machine learning algorithms are currently being implemented in an escalating manner to classify and/or predict the onset of some neurodegenerative diseases; including Alzheimer’s Disease (AD); this could be attributed to the fact of the abundance of data and powerful computers. The objective of this work was to deliver a robust classification system for AD and Mild Cognitive Impairment (MCI) against healthy controls (HC) in a low-cost network in terms of shallow architecture and processing. In this study, the dataset included was downloaded from the Alzheimer’s disease neuroimaging initiative (ADNI). The classification methodology implemented was the convolutional neural network (CNN), where the diffusion maps, and gray-matter (GM) volumes were the input images. The number of scans included was 185, 106, and 115 for HC, MCI and AD respectively. Ten-fold cross-validation scheme was adopted and the stacked mean diffusivity (MD) and GM volume produced an AUC of 0.94 and 0.84, an accuracy of 93.5% and 79.6%, a sensitivity of 92.5% and 62.7%, and a specificity of 93.9% and 89% for AD/HC and MCI/HC classification respectively. This work elucidates the impact of incorporating data from different imaging modalities; i.e. structural Magnetic Resonance Imaging (MRI) and Diffusion Tensor Imaging (DTI), where deep learning was employed for the aim of classification. To the best of our knowledge, this is the first study assessing the impact of having more than one scan per subject and propose the proper maneuver to confirm the robustness of the system. The results were competitive among the existing literature, which paves the …