3D black blood MRI atlases of congenital aortic arch anomalies and the normal fetal heart: application to automated multi-label segmentation

Background 3D image-domain reconstruction of black blood contrast T2w SSTSE fetal MRI datasets using slice-to-volume registration methods showed to provide high-resolution 3D images of the heart with superior visualisation of fetal aortic arch anomalies [[1][1]]. However, there is a lack of formalisation of the MRI appearance of fetal cardiovascular anatomy and standardisation of vessel segmentation protocols. Methods In this work, we present the first set of 3D fetal MRI atlases defining normal and abnormal fetal aortic arch anatomy created from 3D reconstructed images from 87 subjects scanned between 29-34 weeks of gestation with postnatally confirmed outcomes. We also implement and evaluate atlas-guided registration and deep learning (UNETR) methods for automated 3D multi-label fetal heart vessel segmentation. Results We created four atlases representing the average anatomy of the normal fetal heart, coarctation of the aorta, right aortic arch and suspected double aortic arch. Inspection of atlases confirmed the expected pronounced differences in the anatomy of the aortic arch. The results of the multi-label heart vessel UNETR segmentation showed 100% per-vessel detection rate for both normal and abnormal aortic arch anatomy. Conclusions This work introduces the first set of 3D black blood T2w MRI atlases of the normal and abnormal fetal cardiovascular anatomy along with detailed segmentation of the major cardiovascular structures. We also demonstrated the feasibility of using deep learning for multi-label vessel segmentation. ### Competing Interest Statement The authors have declared no competing interest. * DAA : double aortic arch AD : arterial duct AO : aorta ALSA : aberrant left subclavian artery Azy : azygous vein BCA : brachiocephalic artery CoA : coarctation of the aorta CHD : congenital heart disease CNN : convolutional neural networks CMR : cardiac magnetic resonance imaging DAO : descending aorta DSVR : slice-to-volume registration InnV : Innominate vein IVC : inferior vena cava MPA : main pulmonary artery MRI : magnetic resonance imaging LA : left atrium LCCA : left common carotid artery LPA : left pulmonary artery LSA : left subclavian artery LV : left ventricle Pvs : pulmonary veins RA : right artrium RAA : right aortic arch RPA : right pulmonary artery RV : right ventricle SSTSE : single shot turbo spin echo SVC : superior vena cava SVR : slice-to-volume registration [1]: #ref-1