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2 results on '"Lale Umutle"'

1. Automated imaging-based abdominal organ segmentation and quality control in 20,000 participants of the UK Biobank and German National Cohort Studies

Author

Turkay Kart, Marc Fischer, Stefan Winzeck, Ben Glocker, Wenjia Bai, Robin Bülow, Carina Emmel, Lena Friedrich, Hans-Ulrich Kauczor, Thomas Keil, Thomas Kröncke, Philipp Mayer, Thoralf Niendorf, Annette Peters, Tobias Pischon, Benedikt M. Schaarschmidt, Börge Schmidt, Matthias B. Schulze, Lale Umutle, Henry Völzke, Thomas Küstner, Fabian Bamberg, Bernhard Schölkopf, Daniel Rueckert, and Sergios Gatidis

Subjects
Medicine, Science
Abstract

Abstract Large epidemiological studies such as the UK Biobank (UKBB) or German National Cohort (NAKO) provide unprecedented health-related data of the general population aiming to better understand determinants of health and disease. As part of these studies, Magnetic Resonance Imaging (MRI) is performed in a subset of participants allowing for phenotypical and functional characterization of different organ systems. Due to the large amount of imaging data, automated image analysis is required, which can be performed using deep learning methods, e. g. for automated organ segmentation. In this paper we describe a computational pipeline for automated segmentation of abdominal organs on MRI data from 20,000 participants of UKBB and NAKO and provide results of the quality control process. We found that approx. 90% of data sets showed no relevant segmentation errors while relevant errors occurred in a varying proportion of data sets depending on the organ of interest. Image-derived features based on automated organ segmentations showed relevant deviations of varying degree in the presence of segmentation errors. These results show that large-scale, deep learning-based abdominal organ segmentation on MRI data is feasible with overall high accuracy, but visual quality control remains an important step ensuring the validity of down-stream analyses in large epidemiological imaging studies.

Published
2022
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2. Better together: data harmonization and cross-study analysis of abdominal MRI data from UK biobank and the German national cohort

Author

Sergios Gatidis, Turkay Kart, Marc Fischer, Stefan Winzeck, Ben Glocker, Wenjia Bai, Robin Bülow, Carina Emmel, Lena Friedrich, Hans-Ulrich Kauczor, Thomas Keil, Thomas Kröncke, Philipp Mayer, Thoralf Niendorf, Annette Peters, Tobias Pischon, Benedikt M. Schaarschmidt, Börge Schmidt, Matthias B. Schulze, Lale Umutle, Henry Völzke, Thomas Küstner, Fabian Bamberg, Bernhard Schölkopf, Daniel Rueckert, and Innovate UK

Subjects
Nuclear Medicine & Medical Imaging, Cardiovascular and Metabolic Diseases, Medizin, Radiology, Nuclear Medicine and imaging, 1103 Clinical Sciences, General Medicine, Technology Platforms
Abstract

OBJECTIVES: The UK Biobank (UKBB) and German National Cohort (NAKO) are among the largest cohort studies, capturing a wide range of health-related data from the general population, including comprehensive magnetic resonance imaging (MRI) examinations. The purpose of this study was to demonstrate how MRI data from these large-scale studies can be jointly analyzed and to derive comprehensive quantitative image-based phenotypes across the general adult population. MATERIALS AND METHODS: Image-derived features of abdominal organs (volumes of liver, spleen, kidneys, and pancreas; volumes of kidney hilum adipose tissue; and fat fractions of liver and pancreas) were extracted from T1-weighted Dixon MRI data of 17,996 participants of UKBB and NAKO based on quality-controlled deep learning generated organ segmentations. To enable valid cross-study analysis, we first analyzed the data generating process using methods of causal discovery. We subsequently harmonized data from UKBB and NAKO using the ComBat approach for batch effect correction. We finally performed quantile regression on harmonized data across studies providing quantitative models for the variation of image-derived features stratified for sex and dependent on age, height, and weight. RESULTS: Data from 8791 UKBB participants (49.9% female; age, 63 ± 7.5 years) and 9205 NAKO participants (49.1% female, age: 51.8 ± 11.4 years) were analyzed. Analysis of the data generating process revealed direct effects of age, sex, height, weight, and the data source (UKBB vs NAKO) on image-derived features. Correction of data source-related effects resulted in markedly improved alignment of image-derived features between UKBB and NAKO. Cross-study analysis on harmonized data revealed comprehensive quantitative models for the phenotypic variation of abdominal organs across the general adult population. CONCLUSIONS: Cross-study analysis of MRI data from UKBB and NAKO as proposed in this work can be helpful for future joint data analyses across cohorts linking genetic, environmental, and behavioral risk factors to MRI-derived phenotypes and provide reference values for clinical diagnostics.

Published
2022

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