Fully Automated and Standardized Segmentation of Adipose Tissue Compartments by Deep Learning in Three-dimensional Whole-body MRI of Epidemiological Cohort Studies

• URL: http://arxiv.org/abs/2008.02251v1
• Date: Wed, 5 Aug 2020 17:30:14 GMT
• Title: Fully Automated and Standardized Segmentation of Adipose Tissue Compartments by Deep Learning in Three-dimensional Whole-body MRI of Epidemiological Cohort Studies
• Authors: Thomas K\"ustner, Tobias Hepp, Marc Fischer, Martin Schwartz, Andreas Fritsche, Hans-Ulrich H\"aring, Konstantin Nikolaou, Fabian Bamberg, Bin Yang, Fritz Schick, Sergios Gatidis, J\"urgen Machann
• Abstract summary: Quantification and localization of different adipose tissue compartments from whole-body MR images is of high interest to examine metabolic conditions. We propose a 3D convolutional neural network (DCNet) to provide a robust and objective segmentation. Fast (5-7seconds) and reliable adipose tissue segmentation can be obtained with high Dice overlap.
• Score: 11.706960468832301
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: Purpose: To enable fast and reliable assessment of subcutaneous and visceral adipose tissue compartments derived from whole-body MRI. Methods: Quantification and localization of different adipose tissue compartments from whole-body MR images is of high interest to examine metabolic conditions. For correct identification and phenotyping of individuals at increased risk for metabolic diseases, a reliable automatic segmentation of adipose tissue into subcutaneous and visceral adipose tissue is required. In this work we propose a 3D convolutional neural network (DCNet) to provide a robust and objective segmentation. In this retrospective study, we collected 1000 cases (66$\pm$ 13 years; 523 women) from the Tuebingen Family Study and from the German Center for Diabetes research (TUEF/DZD), as well as 300 cases (53$\pm$ 11 years; 152 women) from the German National Cohort (NAKO) database for model training, validation, and testing with a transfer learning between the cohorts. These datasets had variable imaging sequences, imaging contrasts, receiver coil arrangements, scanners and imaging field strengths. The proposed DCNet was compared against a comparable 3D UNet segmentation in terms of sensitivity, specificity, precision, accuracy, and Dice overlap. Results: Fast (5-7seconds) and reliable adipose tissue segmentation can be obtained with high Dice overlap (0.94), sensitivity (96.6%), specificity (95.1%), precision (92.1%) and accuracy (98.4%) from 3D whole-body MR datasets (field of view coverage 450x450x2000mm${}^3$). Segmentation masks and adipose tissue profiles are automatically reported back to the referring physician. Conclusion: Automatic adipose tissue segmentation is feasible in 3D whole-body MR data sets and is generalizable to different epidemiological cohort studies with the proposed DCNet.

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