NETFIO-MS is an innovative medical image analysis tool designed for use with resting-state functional MRI (rsfMRI) to quantitatively assess functional network-based disease burden in MS patients. By focusing on the functional network properties related to neurodegeneration, NETFIO-MS offers a novel approach to the early and accurate diagnosis of MS, as well as the monitoring of disease progression. This tool is based on the functional MACM (fMACM) model, which identifies localized neurodegeneration in MS, marking a significant advancement over traditional methods that primarily focus on demyelinating lesions.