Workflow for automatic renal perfusion quantification using ASL-MRI and machine learning

Isabell K Bones, Clemens Bos, Chrit Moonen, Jeroen Hendrikse, Marijn van Stralen

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Purpose: Clinical applicability of renal arterial spin labeling (ASL) MRI is hampered because of time consuming and observer dependent post-processing, including manual segmentation of the cortex to obtain cortical renal blood flow (RBF). Machine learning has proven its value in medical image segmentation, including the kidneys. This study presents a fully automatic workflow for renal cortex perfusion quantification by including machine learning-based segmentation. Methods: Fully automatic workflow was achieved by construction of a cascade of 3 U-nets to replace manual segmentation in ASL quantification. All 1.5T ASL-MRI data, including M 0, T 1, and ASL label-control images, from 10 healthy volunteers was used for training (dataset 1). Trained cascade performance was validated on 4 additional volunteers (dataset 2). Manual segmentations were generated by 2 observers, yielding reference and second observer segmentations. To validate the intended use of the automatic segmentations, manual and automatic RBF values in mL/min/100 g were compared. Results: Good agreement was found between automatic and manual segmentations on dataset 1 (dice score = 0.78 ± 0.04), which was in line with inter-observer variability (dice score = 0.77 ± 0.02). Good agreement was confirmed on dataset 2 (dice score = 0.75 ± 0.03). Moreover, similar cortical RBF was obtained with automatic or manual segmentations, on average and at subject level; with 211 ± 31 mL/min/100 g and 208 ± 31 mL/min/100 g (P <.05), respectively, with narrow limits of agreement at −11 and 4.6 mL/min/100 g. RBF accuracy with automated segmentations was confirmed on dataset 2. Conclusion: Our proposed method automates ASL quantification without compromising RBF accuracy. With quick processing and without observer dependence, renal ASL-MRI is more attractive for clinical application as well as for longitudinal and multi-center studies.

Original languageEnglish
Pages (from-to)800-809
Number of pages10
JournalMagnetic Resonance in Medicine
Issue number2
Early online date20 Oct 2021
Publication statusPublished - Feb 2022


  • automatic ASL quantification
  • automatic segmentation
  • machine learning
  • RBF
  • renal ASL MRI


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