Despite recent advances in tractography, automatically reconstructing brain bundles in clinical settings remains a challenge. Here we present Q-FiberMapper (QFM), a framework that automatically preprocesses clinical data and reconstructs 33 major brain bundles with minimal user intervention. Furthermore, it derives insightful biomarkers and summarizes the findings in a human readable report. We validate QFM using a large cohort of 600 subjects, and show that it correctly reconstructs the shape and lateralization of major white-matter bundles. By simplifying and speeding the process of clinical reconstruction, QFM could help clinicians in the diagnosis and monitoring of brain pathologies.
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