Analysis of aorta hemodynamics is useful in the evaluation of aortic diseases. 4D PC-MRI provides information of flow velocity in the aorta and automatic segmentation is one of the biggest challenges. We propose a fully 3D automatic segmentation of the aorta in systole using a multi-atlas approach. Evaluation on 16 patients provided an average performance of 29.55±24.33 mm and 0.859 ±0.024 for Hausdorff distance and Dice score respectively. With the proposed method, the automatic segmentation of the thoracic aorta that can be obtained from 4D PC-MRI is close enough to the manual one to be used in future studies.