arXiv subjects

Bene Wiestler

Publications and source records attributed to Bene Wiestler.

3 recordsLinked to original sources

arXiv2024

VIBESegmentator: Full Body MRI Segmentation for the NAKO and UK Biobank

Objectives: To present a publicly available deep learning-based torso segmentation model that provides comprehensive voxel-wise coverage, including delineations that extend to the boundaries of anatomical compartments. Materials and Methods: We extracted preliminary segmentations from TotalSegmentator, spine, and body composition models for Magnetic Resonance Tomography (MR) images, then improved them iteratively and retrained an nnUNet model. Using a random retrospective subset of German National Cohort (NAKO), UK Biobank, internal MR and Computed Tomography (CT) data (Training: 2897 series from 626 subjects, 290 female; mean age 53+-16; 3-fold-cross validation (20% hold-out). Internal testing 36 series from 12 subjects, 6 male; mean age 60+-11), we segmented 71 structures in torso MR and 72 in CT images: 20 organs, 10 muscles, 19 vessels, 16 bones, ribs in CT, intervertebral discs, spinal cord, spinal canal and body composition (subcutaneous fat, unclassified muscles and visceral fat). For external validation, we used existing automatic organ segmentations, independent ground truth segmentations on gradient echo images, and the Amos data. We used non-parametric bootstrapping for confidence intervals and Wilcoxon rank-sum test for computing statistical significance. Results: We achieved an average Dice score of 0.90+-0.06 on our internal gradient echo test set, which included 71 semantic segmentation labels. Our model ties with the best model on Amos with a Dice of 0,81+-0.14, while having a larger field of view and a considerably higher number structures included. Conclusion: Our work presents a publicly available full-torso segmentation model for MRI and CT images that classifies almost all subject voxels to date.

eess.IV↗

arXiv2023

Individualizing Glioma Radiotherapy Planning by Optimization of Data and Physics-Informed Discrete Loss

Brain tumor growth is unique to each glioma patient and extends beyond what is visible in imaging scans, infiltrating surrounding brain tissue. Understanding these hidden patient-specific progressions is essential for effective therapies. Current treatment plans for brain tumors, such as radiotherapy, typically involve delineating a uniform margin around the visible tumor on pre-treatment scans to target this invisible tumor growth. This "one size fits all" approach is derived from population studies and often fails to account for the nuances of individual patient conditions. We present the GliODIL framework, which infers the full spatial distribution of tumor cell concentration from available multi-modal imaging, leveraging a Fisher-Kolmogorov type physics model to describe tumor growth. This is achieved through the newly introduced method of Optimizing the Discrete Loss, where both data and physics-based constraints are softly assimilated into the solution. Our test dataset comprises 152 glioblastoma patients with pre-treatment imaging and post-treatment follow-ups for tumor recurrence monitoring. By blending data-driven techniques with physics-based constraints, GliODIL enhances recurrence prediction in radiotherapy planning, challenging traditional uniform margins and strict adherence to the Fisher-Kolmogorov partial differential equation model, which is adapted for complex cases.

physics.med-ph↗

arXiv2022

CheXplaining in Style: Counterfactual Explanations for Chest X-rays using StyleGAN

Deep learning models used in medical image analysis are prone to raising reliability concerns due to their black-box nature. To shed light on these black-box models, previous works predominantly focus on identifying the contribution of input features to the diagnosis, i.e., feature attribution. In this work, we explore counterfactual explanations to identify what patterns the models rely on for diagnosis. Specifically, we investigate the effect of changing features within chest X-rays on the classifier's output to understand its decision mechanism. We leverage a StyleGAN-based approach (StyleEx) to create counterfactual explanations for chest X-rays by manipulating specific latent directions in their latent space. In addition, we propose EigenFind to significantly reduce the computation time of generated explanations. We clinically evaluate the relevancy of our counterfactual explanations with the help of radiologists. Our code is publicly available.

eess.IV↗