Automation of Kidney Perfusion Analysis from Dynamic Phase-Contrast MRI using Deep Learning

Sammanfattning: Renal phase-contrast magnetic resonance imaging (PC-MRI) is an MRI modality where the phase component of the MR signal is made sensitive to the velocity of water molecules in the kidneys. PC-MRI is able to assess the Renal Blood Flow (RBF), which is an important biomarker in the development of kidney disease. RBF is analyzed with the manual or semi-automatic delineation by experts of the renal arteries in PC-MRI. This is a time-consuming and operator-dependent process. We have therefore trained, validated and tested a fully-automated deep learning model for faster and more objective renal artery segmentation. The PC-MRI data used in model training, validation and testing come from four studies (N=131 subjects). Images were acquired from three manufacturers with different imaging parameters. The best deep learning model found consists of a deeply-supervised 2D attention U-Net with residual skip connections. The output of this model was re-introduced as an extra channel in a second iteration to refine the segmentation result. The flow values in the segmented regions were integrated to provide a quantification of the mean arterial flow in the segmented renal arteries. The automated segmentation was evaluated in all the images that had manual segmentation ground-truths that come from a single operator. The evaluation was completed in terms of a segmentation accuracy metric called Dice Coefficient. The mean arterial flow values that were quantified from the auto-mated segmentation were also evaluated against ground-truth flow values from semi-automatic software. The deep learning model was trained and validated on images with segmentation ground-truths with 4-fold cross-validation. A Dice segmentation accuracy of 0.71±0.21 was achieved (N=73 subjects). Although segmentation results were accurate for most arteries, the algorithm failed in ten out of 144arteries. The flow quantification from the segmentation was highly correlated without significant bias in comparison to the ground-truth flow measurements. This method shows promise for supporting RBF measurements from PC-MRI and can likely be used to save analysis time in future studies. More training data has to be used for further improvement, both in terms of accuracy and generalizability.