Manual sinus magnetic resonance imaging (MRI) annotations are valuable but difficult to scale. We evaluated PARASIDE, an nnU-Net-based framework for automated sinus compartment segmentation on T1-weighted MRI, against independent manual and radiological assessments from the Study of Health in Pomerania. We linked 12,867 sinus sides from 3,217 participants. Analyses defined before outcome modelling evaluated soft-tissue fraction for healthy versus abnormal sides, inferior soft-tissue centroid position for basal versus apical maxillary opacification, and total frontal volume for aplasia/hypoplasia. Soft-tissue fraction discriminated abnormal sides in frontal (area under the receiver operating characteristic curve [AUC] 0.850, 95% confidence interval [CI] 0.834–0.866) and maxillary sinuses (AUC 0.828, 95% CI 0.818–0.839). The topographic marker discriminated basal from apical opacification (AUC 0.746 left; 0.782 right). Total frontal volume discriminated historical aplasia/hypoplasia ratings (AUC 0.988); a previously established near-absence threshold was highly specific but insensitive. Historical maxillary volumetric masks showed strong overlap and volume association for total and aerated compartments, whereas frontal comparisons reflected a predefined caudal boundary. The historical polyposis rating category remained weakly separable, and surgery-related features corresponded more closely to visible postoperative morphology than to self-reported surgery. PARASIDE reproduced anatomically measurable MRI phenotypes, whereas morphology-specific constructs required dedicated reference standards.

Manual sinus magnetic resonance imaging (MRI) annotations are valuable but difficult to scale. We evaluated PARASIDE, an nnU-Net-based framework for automated sinus compartment segmentation on T1-weighted MRI, against historical manual annotations and radiological assessments generated independently of PARASIDE within the same longitudinal Study of Health in Pomerania (SHIP) imaging population. We linked 12,867 sinus sides from 3217 participants. Primary construct–marker pairings were specified before endpoint-specific modelling. Soft-tissue fraction discriminated abnormal sides in frontal (AUC 0.850, 95% CI 0.832–0.868) and maxillary sinuses (AUC 0.828, 95% CI 0.816–0.841). The topographic marker showed moderate discrimination of basal from apical opacification (AUC 0.746 left; 0.782 right), while total frontal volume discriminated aplasia/hypoplasia ratings (AUC 0.988); the near-absence threshold remained highly specific but insensitive. Primary findings were robust to exclusion of 279 participants overlapping with the original PARASIDE development population. Historical maxillary volumetric masks showed strong agreement, whereas frontal agreement improved after accounting for the predefined inferior extent of the non-equivalent historical segmentation approach. Polyposis remained weakly separable. PARASIDE showed correspondence with distinct, anatomically measurable MRI phenotypes across complementary historical reference layers, while morphology-specific constructs required dedicated reference standards.