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Background  Accurate measurement of left atrial (LA) volumes is needed in cardiac diagnostics and the follow up of heart and valvular diseases. Geometrical assumptions with 2D methods for LA volume estimation contribute to volume misestimation. In this study, we test agreement of 3D and 2D methods of LA volume detection and explore contribution of 3D LA axis orientation and LA shape in introducing error in 2D methods by cardiovascular magnetic resonance imaging.    Methods  30 patients with prior first-ever ischemic stroke and no known heart disease, and 30 healthy controls were enrolled (age 18–49) in a substudy of a prospective case–control study. All study subjects underwent cardiac magnetic resonance imaging and were pooled for this methodological study. LA volumes were calculated by biplane area-length method from both conventional long axis (LAV AL-LV ) and LA long axis-oriented images (LAV AL-LA ) and were compared to 3D segmented LA volume (LAV SAX ) to assess accuracy of volume detection. 3D orientation of LA long axis to left ventricular (LV) long axis and to four-chamber plane were determined, and LA 3D sphericity indices were calculated to assess sources of error in LA volume calculation. Shapiro–Wilk test, Bland–Altman analysis, intraclass and Pearson correlation, and Spearman’s rho were used for statistical analysis.    Results  Biases were − 9.9 mL (− 12.5 to − 7.2) for LAV AL-LV  and 13.4 (10.0–16.9) for LAV AL-LA  [mean difference to LAV SAX  (95% confidence interval)]. End-diastolic LA long axis 3D deviation angle to LV long axis was 28.3 ± 6.2° [mean ± SD] and LA long axis 3D rotation angle to four-chamber plane 20.5 ± 18.0°. 3D orientation of LA axis or 3D sphericity were not correlated to error in LA volume calculation.    Conclusions  Calculated LA volume accuracy did not improve by using LA long axis-oriented images for volume calculation in comparison to conventional method. We present novel data on LA axis orientation and a novel metric of LA sphericity and conclude that these measures cannot be utilized to assess error in LA volume calculation.Trial registration   Main study Searching for Explanations for Cryptogenic Stroke in the Young: Revealing the Etiology, Triggers, and Outcome (SECRETO; NCT01934725) has been registered previously.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12880-021-00701-5.

Revisiting left atrial volumetry by magnetic resonance imaging: the role of atrial shape and 3D angle between left ventricular and left atrial axis