NeuroHarm‑Kit: An open‑source toolbox for benchmarking deep‑learning harmonization of multi‑site T1‑weighted MRI

Multi‑site magnetic resonance imaging (MRI) studies enable studying brain structure across diverse populations, but scanner‑related variability remains a critical barrier to pooled analyses. Here, we introduce NeuroHarm‑Kit, the first open‑source, end‑to‑end toolbox that unifies state‑of‑the‑art deep‑learning harmonization models (STGAN, HACA3, MURD, DISARM++, IGUANe) for 3D T1‑weighted scans. NeuroHarm‑Kit provides standardized preprocessing and pretrained weights, thereby enabling reproducible, head‑to‑head comparisons. Applied to traveling‑subject and healthy aging cohorts, NeuroHarm‑Kit demonstrates that different methods excel in distinct metrics: some optimize intensity‑distribution alignment, others preserve anatomical fidelity or biological information. No single approach uniformly outperforms across all criteria, underscoring the need to tailor harmonization choices to specific research objectives. The toolbox provides researchers with a ready-to-use framework to compare harmonization strategies and select the most appropriate method for their data and study design. With its modular design, NeuroHarm‑Kit can be extended to additional modalities and new methods. By lowering methodological barriers and promoting transparent benchmarking, this toolbox aims to accelerate innovation and reproducibility in multi‑site neuroimaging harmonization. GitHub project is available at https://github.com/barna-hache/NeuroHarm-kit.