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Amyotrophic Lateral Sclerosis (ALS) is a complex neurodegenerative disorder involving motor neuron degeneration. Significant research has begun to establish brain magnetic resonance imaging (MRI) as a potential biomarker to diagnose and monitor the state of the disease. Deep learning has turned into a prominent class of machine learning programs in computer vision and has been successfully employed to solve diverse medical image analysis tasks. However, deep learning-based methods applied to neuroimaging have not achieved superior performance in ALS patients classification from healthy controls due to having insignificant structural changes correlated with pathological features. Therefore, the critical challenge in deep models is to determine useful discriminative features with limited training data. By exploiting the long-range relationship of image features, this study introduces a framework named SF2Former that leverages vision transformer architecture's power to distinguish the ALS subjects from the control group. To further improve the network's performance, spatial and frequency domain information are combined because MRI scans are captured in the frequency domain before being converted to the spatial domain. The proposed framework is trained with a set of consecutive coronal 2D slices, which uses the pre-trained weights on ImageNet by leveraging transfer learning. Finally, a majority voting scheme has been employed to those coronal slices of a particular subject to produce the final classification decision. Our proposed architecture has been thoroughly assessed with multi-modal neuroimaging data using two well-organized versions of the Canadian ALS Neuroimaging Consortium (CALSNIC) multi-center datasets. The experimental results demonstrate the superiority of our proposed strategy in terms of classification accuracy compared with several popular deep learning-based techniques., Comment: 17 pages, 8 figures