MALINI (Machine Learning in NeuroImaging): A MATLAB toolbox for aiding clinical diagnostics using resting-state fMRI data

Abstract Resting-state functional Magnetic Resonance Imaging (Rs-fMRI) has been extensively used for diagnostic classification because it does not require task compliance and is easier to pool data from multiple imaging sites, thereby increasing the sample size. A MATLAB-based toolbox called Machine Learning in NeuroImaging (MALINI) for feature extraction and disease classification is presented. The MALINI toolbox extracts functional and effective connectivity features from preprocessed Rs-fMRI data and performs classification between healthy and disease groups using 18 popular and widely used machine learning algorithms that are based on diverse principles. A consensus classifier combining the power of multiple classifiers is also presented. The utility of the toolbox is illustrated by accompanying data consisting of resting-state functional connectivity features from healthy controls and subjects with various brain-based disorders: autism spectrum disorder from autism brain Image data exchange (ABIDE), Alzheimer’s disease and mild-cognitive impairment from Alzheimer’s disease neuroimaging initiative (ADNI), attention deficit hyperactivity disorder from ADHD-200, and post-traumatic stress disorder and post-concussion syndrome acquired in-house. Results of the classifiers on the above datasets can be obtained from the main article titled “Supervised machine learning for diagnostic classification from large-scale neuroimaging datasets” [1]. The data was divided into homogeneous and heterogeneous splits, such that 80% can be used for training, model building and cross-validation, while the remaining 20% of the data could be used as a hold-out independent test data for replication of the classification performance to ensure the robustness of the classifiers to population variance in image acquisition site and age of the sample.