MRSIPrep: A Standardized Post-Quantification Framework for Preprocessing Whole-Brain Magnetic Resonance Spectroscopic Imaging

Abstract

Magnetic resonance spectroscopic imaging (MRSI) enables non-invasive mapping of neu-rometabolites levels across the human brain. Although spectral fitting and metabolite quan-tification are increasingly supported by mature software tools, the downstream processing of quantified metabolite maps remains heterogeneous across laboratories. Here, we introduce MRSIPrep, an open-source, modular, and reproducible post-quantification framework for whole-brain MRSI. MRSIPrep standardizes quality control, tissue correction, spatial nor- malization, atlas projection, and derivative generation from quantified metabolite maps and associated quality metrics. The framework produces voxelwise, regional, and connectomics-ready outputs together with automated quality-control reports. We describe the architecture of MRSIPrep and demonstrate its utility for reproducible MRSI analysis across datasets,acquisition protocols, and downstream applications.