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Accurate quantification of left ventricular mass and ejection fraction is important for patients with left ventricular hypertrophy. Although cardiac magnetic resonance imaging has been proposed as a standard for these indices, prior studies have variably included papillary muscles and trabeculae in myocardial volume. This study investigated the contribution of papillary muscles and trabeculae to left ventricular quantification in relation to the presence and pattern of hypertrophy.Cardiac magnetic resonance quantification was performed on patients with concentric or eccentric hypertrophy and normal controls (20 per group) using two established methods that included papillary muscles and trabeculae in myocardium (method 1) or intracavitary (method 2) volumes.Among all patients, papillary muscles and trabeculae accounted for 10.5% of ventricular mass, with greater contribution with left ventricular hypertrophy than normals (12.6 vs. 6.2%, P < 0.001). Papillary muscles and trabeculae mass correlated with ventricular wall mass (r = 0.53) and end-diastolic volume (r = 0.52; P < 0.001). Papillary muscles and trabeculae inclusion in myocardium (method 1) yielded smaller differences with a standard of mass quantification from linear ventricular measurements than did method 2 (P < 0.001). Method 1 in comparison with method 2 yielded differences in left ventricular mass, ejection fraction and volume in all groups, especially in patients with hypertrophy: the difference in ventricular mass index was three-fold to six-fold greater in hypertrophy than normal groups (P < 0.001). Difference in ejection fraction, greatest in concentric hypertrophy (P < 0.001), was independently related to papillary muscles and trabeculae mass, ventricular wall mass, and smaller ventricular volume (R2 = 0.56, P < 0.001).Established cardiac magnetic resonance methods yield differences in left ventricular quantification due to variable exclusion of papillary muscles and trabeculae from myocardium. The relative impact of papillary muscles and trabeculae exclusion on calculated mass and ejection fraction is increased among patients with hypertrophy-associated left ventricular remodeling.