Automatic segmentation of the aorta on multi-center and multi-vendor phase-contrast enhanced magnetic resonance angiographies and the advantages of transfer learning
Authors: Aviles J , Maso Talou G , Camara O , Mejia Cordova M , Ferdian E , Kat G , Young A , Dux-Santoy L , Ruiz-Munoz A , Teixido-Tura G , Rodriguez-Palomares J , Guala A 
Published: July 2021

Abstract

Funding Acknowledgements
Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Guala A. received funding from the Spanish Ministry of Science, Innovation and Universities

Background
Phase-contrast (PC) enhanced magnetic resonance (MR) angiography (MRA) is a class of angiogram exploiting velocity data to increase the signal-to-noise ratio, thus avoiding the administration of external contrast agent, normally used to segment 4D flow MR data. To train deep-learning algorithms to segment PC-MRA a large amount of manually annotated data is needed: however, the relatively novelty of the sequence, its rapid evolution and the extensive time needed to manually segment data limit its availability.

Purpose
The aim of this study was to test a deep learning algorithm in the segmentation of multi-center and multi-vendor PC-MRA and to test if transfer learning (TL) improves performance.

Methods
A large dataset (LD) of 262 and a small one (SD) of 22 PC-MRA, acquired without contrast agent at 1.5 T in a General Electric and a Siemens scanner, respectively, were manually annotated and divided into training (232 and 15 cases) and testing (30 and 7) sets. They both included PC-MRA of healthy subjects and patients with aortic diseases (excluding dissections) and native aorta. A convolutional neural networks (CNN) based on nnU-Net framework [1] was trained in the LD and another in the SD. The left ventricle was removed semi-automatically from the DL segmentations of the LD as it was not relevant for this application. Networks were then tested on the test sets of the dataset there were trained and the other dataset to assess generalizability. Finally, a fine-tuning transfer learning approach was applied to LD network and the performance on both test sets were tested. Dice score, Hausdorff distance, Jaccard score and Average Symmetrical Surface Distance were used as segmentation quality metrics.

Results
LD network achieved good performance in LD test set, with a DS of 0.904, ASSD of 1.47, J of 0.827 and HD of 6.35, which further improve after removing the left ventricle in the post-processing to a DS of 0.942, ASSD of 0.93, J of 0.892 and HD of 3.32. SD network results in an average DS of 0.895, ASSD of 0.59, J of 0.812 and HD of 2.05. Once tested on the testing set of the other dataset, LD network resulted in a DS of 0.612 while SD network in DS of 0.375, thus showing limited generalizability. However, the application of transfer learning to LD network resulted in the improvement of the evaluation metrics on the SD from a DS of 0.612 to 0.858, while slightly worsening in the first one without post-processing to 0.882.

Conclusions
nnU-net framework is effective for fast automatic segmentation of the aorta from multi-center and multi-vendor PC-MRA, showing performance comparable with the state of the art. The application of transfer learning allows for increased generalization to data from center not included in the original training. These results unlock the possibility for fully-automatic analysis of multi-vendor multi-center 4D flow MR.