PURPOSE: 3D free-breathing, proton, contrast-agent-free MR methods are increasingly used for pulmonary ventilation-weighted measurements. The methods are split between: (1) signal-based, which rely on lung parenchyma signal changes during respiration, and (2) volume-based that utilize the Jacobian determinant of deformation fields from the image registration. This study compares both proton methods using respiratory-resolved images acquired using fermat-looped orthogonally encoded trajectories (FLORET) acquisition. METHODS: Free-breathing FLORET data were acquired from participants with various pulmonary conditions (N = 29) and healthy controls (N = 7), and reconstructed into respiratory phase-resolved images. Signal-based regional ventilation (RVent) was quantified using the 3D phase-resolved functional lung algorithm, and volume-based Jacobian ventilation (JVent) was derived as the Jacobian of the deformation field from the direct image registration of the end-expiratory image to the end-inspiratory image. Differences between the means, coefficients of variation (CoVs), and their ventilation defect percent (VDP) were quantified by Bland-Altman plots. The spatial overlap of the defect maps was determined by multi-class Sørensen-Dice coefficient, and Spearman correlations to (129)Xe MRI were assessed. RESULTS: In all study participants, statistically significant differences were found between means/CoVs of RVent and JVent parameters (both p < 0.0001), but not VDP (p = 0.38). The median spatial overlap of the defect maps was 86%. VDP(RVent) showed stronger correlation (
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