BrainInsights: a comprehensive framework for pre-processing, analysis, and interpretation of neuroimaging data using traditional statistics and machine learning

Neuroimaging presents us with an in-depth understanding about brain structure and function, yet the data complexity poses significant analytical challenges. Current frameworks suffer from issues such as scalability, poor integration with traditional statistics and a need for a programing background, which hinder researchers from focusing on neuroscience questions. To address these limitations, we present BrainInsights, an integrated and automated GUI-based pipeline ecosystem designed to facilitate the analysis of multi-modal or multi-parametric neuroimaging data in a flexible way. The framework comprises three core tools: MARIA (MAgnetic Resonance Imaging data Analysis and inspection tool) for data inspection and hypotheses testing, ML Pipeline for automated feature selection and model construction, and ML DaViz for model evaluation and bio-signature generation. Deployed as a singularity container, the system ensures reproducibility and scalability across computing environments. We validated BrainInsights using diverse datasets, including multi-parametric MRI studies of Anorexia Nervosa, Crohn’s disease, and Rheumatoid Arthritis. Specifically, the framework distinguished young Anorexia Nervosa patients from controls with a balanced accuracy of 65%, while in the PreCePRA trial, it predicted Rheumatoid Arthritis treatment response with a balanced accuracy of up to 95.4% using functional pain markers. The results demonstrate the ability of the framework to achieve high separation of subgroups and treatment success and additionally bridge hypotheses-driven statistical analysis with data-driven machine learning analysis. By enabling interpretability tools like SHAP, BrainInsights empowers researchers to move beyond “black-box” modeling to uncover stable, biologically plausible bio-signatures. Ultimately, this framework aids in accelerating the translation of complex neuroimaging data into meaningful clinical insights.