05 Fakultät Informatik, Elektrotechnik und Informationstechnik

Permanent URI for this collectionhttps://elib.uni-stuttgart.de/handle/11682/6

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Institute: search.filters.UBSInstitut.Institut für Signalverarbeitung und SystemtheorieAuthor: search.filters.author.Bamberg, Fabian

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    Automated imaging-based abdominal organ segmentation and quality control in 20,000 participants of the UK Biobank and German National Cohort Studies
    (2022) Kart, Turkay; Fischer, Marc; Winzeck, Stefan; Glocker, Ben; Bai, Wenjia; Bülow, Robin; Emmel, Carina; Friedrich, Lena; Kauczor, Hans-Ulrich; Keil, Thomas; Kröncke, Thomas; Mayer, Philipp; Niendorf, Thoralf; Peters, Annette; Pischon, Tobias; Schaarschmidt, Benedikt M.; Schmidt, Börge; Schulze, Matthias B.; Umutle, Lale; Völzke, Henry; Küstner, Thomas; Bamberg, Fabian; Schölkopf, Bernhard; Rückert, Daniel; Gatidis, Sergios
    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.
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    Identification of radiomic biomarkers in a set of four skeletal muscle groups on Dixon MRI of the NAKO MR study
    (2023) Fischer, Marc; Küstner, Thomas; Pappa, Sofia; Niendorf, Thoralf; Pischon, Tobias; Kröncke, Thomas; Bette, Stefanie; Schramm, Sara; Schmidt, Börge; Haubold, Johannes; Nensa, Felix; Nonnenmacher, Tobias; Palm, Viktoria; Bamberg, Fabian; Kiefer, Lena; Schick, Fritz; Yang, Bin
    In this work, we propose a processing pipeline for the extraction and identification of meaningful radiomics biomarkers in skeletal muscle tissue as displayed using Dixon-weighted MRI. Diverse and robust radiomics features can be identified that may be of aid in the accurate quantification e.g. varying degrees of sarcopenia in respective muscles of large cohorts. As such, the approach comprises the texture feature extraction from raw data based on well established approaches, such as a nnU-Net neural network and the Pyradiomics toolbox, a subsequent selection according to adequate conditions for the muscle tissue of the general population, and an importance-based ranking to further narrow the amount of meaningful features with respect to auxiliary targets. The performance was investigated with respect to the included auxiliary targets, namely age, body mass index (BMI), and fat fraction (FF). Four skeletal muscles with different fiber architecture were included: the mm. glutaei, m. psoas, as well as the extensors and adductors of the thigh. The selection allowed for a reduction from 1015 available texture features to 65 for age, 53 for BMI, and 36 for FF from the available fat/water contrast images considering all muscles jointly. Further, the dependence of the importance rankings calculated for the auxiliary targets on validation sets (in a cross-validation scheme) was investigated by boxplots. In addition, significant differences between subgroups of respective auxiliary targets as well as between both sexes were shown to be present within the ten lowest ranked features by means of Kruskal-Wallis H-tests and Mann-Whitney U-tests. The prediction performance for the selected features and the ranking scheme were verified on validation sets by a random forest based multi-class classification, with strong area under the curve (AUC) values of the receiver operator characteristic (ROC) of 73.03 ± 0.70 % and 73.63 ± 0.70 % for the water and fat images in age, 80.68 ± 0.30 % and 88.03 ± 0.89 % in BMI, as well as 98.36 ± 0.03 % and 98.52 ± 0.09 % in FF.