Receive a weekly summary and discussion of the top papers of the week by leading researchers in the field.

In Journal of magnetic resonance imaging : JMRI

BACKGROUND : Axonal loss denervates muscle, leading to an increase of fat accumulation in the muscle. Therefore, fat fraction (FF) in whole limb muscle using MRI has emerged as a monitoring biomarker for axonal loss in patients with peripheral neuropathies. In this study, we are testing whether deep learning-based model can automate quantification of the FF in individual muscles. While individual muscle is smaller with irregular shape, manually segmented muscle MRI images have been accumulated in this lab; and make the deep learning feasible.

PURPOSE : To automate segmentation on muscle MRI images through deep learning for quantifying individual muscle FF in patients with peripheral neuropathies.

STUDY TYPE : Retrospective.

SUBJECTS : 24 patients and 19 healthy controls.


ASSESSMENT : A 3D U-Net model was implemented in segmenting muscle MRI images. This was enabled by leveraging a large set of manually segmented muscle MRI images. B1+ and B1- maps were used to correct image inhomogeneity. Accuracy of the automation was evaluated using Pixel Accuracy (PA), Dice Coefficient (DC) in binary masks; and Bland-Altman and Pearson correlation by comparing FF values between manual and automated methods.

STATISTICAL TESTS : PA and DC were reported with their median value and standard deviation. Two methods were compared using the ± 95% confidence intervals (CI) of Bland-Altman analysis and the Pearson's coefficient (r2 ).

RESULTS : DC values were from 0.83 ± 0.17 to 0.98 ± 0.02 in thigh and from 0.63 ± 0.18 to 0.96 ± 0.02 in calf muscles. For FF values, the overall ± 95% CI and r2 were [0.49, -0.56] and 0.989 in thigh and [0.84, -0.71] and 0.971 in the calf.

DATA CONCLUSION : Automated results well agreed with the manual results in quantifying FF for individual muscles. This method mitigates the formidable time consumption and intense labor in manual segmentations; and enables the use of individual muscle FF as outcome measures in upcoming longitudinal studies.


Chen Yongsheng, Moiseev Daniel, Kong Wan Yee, Bezanovski Alexandar, Li Jun


Dixon magnetic resonance imaging, axonal loss, convolutional neural network, fat fraction, muscle, peripheral neuropathy