Automated liver magnetic resonance elastography quality control and liver stiffness measurement using deep learning

Abstract

Purpose

Magnetic resonance elastography (MRE) measures liver stiffness for fibrosis staging, but its utility can be hindered by quality control (QC) challenges and measurement variability. The objective of the study was to fully automate liver MRE QC and liver stiffness measurement (LSM) using a deep learning (DL) method.

Methods

In this retrospective, single center, IRB-approved human study, a curated dataset involved 897 MRE magnitude slices from 146 2D MRE scans [1.5 T and 3 T MRI, 2D Gradient Echo (GRE), and 2D Spin Echo-Echo Planar Imaging (SE-EPI)] of 69 patients (37 males, mean age 51.6 years). A SqueezeNet-based binary QC model was trained using combined and individual inputs of MRE magnitude slices and their 2D Fast-Fourier transforms to detect artifacts from patient motion, aliasing, and blurring. Three independent observers labeled MRE magnitude images as 0 (non-diagnostic quality) or 1 (diagnostic quality) to create a reference standard. A 2D U-Net segmentation model was trained on diagnostic slices with liver masks to support LSM. Intersection over union between the predicted segmentation and confidence masks identified measurable areas for LSM on elastograms. Cohen’s unweighted Kappa coefficient, mean LSM error (%), and intra-class correlation coefficient were calculated to compare the DL-assisted approach with the observers’ annotations. An efficiency analysis compared the DL-assisted vs manual LSM durations.

Results

The top QC ensemble model (using MRE magnitude alone) achieved accuracy, precision, and recall of 0.958, 0.982, and 0.886, respectively. The mean LSM error between the DL-assisted approach and the reference standard was 1.9% ± 4.6%. DL-assisted approach completed LSM for 29 diagnostic slices in under 1 s, compared to 20 min manually.

Conclusion

An automated DL-based classification of liver MRE diagnostic quality, liver segmentation, and LSM approach demonstrates a promising high performance, with potential for clinical adoption.