Hartmut Häntze

Hartmut Häntze, Sarah de Boer, Myrthe Buser et al.

The rapid proliferation of open-source medical foundation models (FMs) raises a practical question: how well do their pre-trained representations transfer to clinically relevant but data-scarce classification tasks? Particularly in CT-based renal lesion classification, a push toward greater generalizability would be meaningful, as the field is constrained by inherently limited training data. We addressed this through a benchmark of three medical FMs on this specific task. This six-class problem spans common entities like cysts and clear cell renal cell carcinoma, alongside rare subtypes. Using a frozen feature-probing protocol, we compared FM embeddings against a handcrafted radiomics classifier and a 3D ResNet-50 trained from scratch. Models were trained on a composite dataset of 2,854 lesions and evaluated on an external test set of 234 lesions from The Cancer Imaging Archive. Our results reveal two key findings. First, FM performance (AUC 0.70-0.77) matched the from-scratch ResNet (AUC 0.72) while drastically reducing hardware demand, requiring only seconds on a CPU after feature extraction. However, the conventional radiomics baseline significantly outperformed all deep learning approaches, achieving an AUC of 0.88 (all p $\leq$ 0.002). This suggests that current generalist FM embeddings do not yet capture the fine-grained texture and shape heterogeneity driving histological subtype discrimination. Despite their potential in data-scarce settings, medical FMs did not surpass established models for renal lesion stratification, leaving radiomics as the current state-of-the-art.

Hartmut Häntze, Lina Xu, Christian J. Mertens et al.

Purpose: To develop and evaluate a deep learning model for multi-organ segmentation of MRI scans. Materials and Methods: The model was trained on 1,200 manually annotated 3D axial MRI scans from the UK Biobank, 221 in-house MRI scans, and 1228 CT scans from the TotalSegmentator dataset. A human-in-the-loop annotation workflow was employed, leveraging cross-modality transfer learning from an existing CT segmentation model to segment 40 anatomical structures. The annotation process began with a model based on transfer learning between CT and MR, which was iteratively refined based on manual corrections to predicted segmentations. The model's performance was evaluated on MRI examinations obtained from the German National Cohort (NAKO) study (n=900) from the AMOS22 dataset (n=60) and from the TotalSegmentator-MRI test data (n=29). The Dice Similarity Coefficient (DSC) and Hausdorff Distance (HD) were used to assess segmentation quality, stratified by organ and scan type. The model and its weights will be open-sourced. Results: MRSegmentator demonstrated high accuracy for well-defined organs (lungs: DSC 0.96, heart: DSC 0.94) and organs with anatomic variability (liver: DSC 0.96, kidneys: DSC 0.95). Smaller structures showed lower accuracy (portal/splenic veins: DSC 0.64, adrenal glands: DSC 0.69). On external validation using NAKO data, mean DSC ranged from 0.85 $\pm$ 0.08 for T2-HASTE to 0.91 $\pm$ 0.05 for in-phase sequences. The model generalized well to CT, achieving mean DSC of 0.84 $\pm$ 0.11 on AMOS CT data. Conclusion: MRSegmentator accurately segments 40 anatomical structures in MRI across diverse datasets and imaging protocols, with additional generalizability to CT images. This open-source model will provide a valuable tool for automated multi-organ segmentation in medical imaging research. It can be downloaded from https://github.com/hhaentze/MRSegmentator.

Sarah de Boer, Hartmut Häntze, Kiran Vaidhya Venkadesh et al.

Kidney abnormality segmentation has important potential to enhance the clinical workflow, especially in settings requiring quantitative assessments. Kidney volume could serve as an important biomarker for renal diseases, with changes in volume correlating directly with kidney function. Currently, clinical practice often relies on subjective visual assessment for evaluating kidney size and abnormalities, including tumors and cysts, which are typically staged based on diameter, volume, and anatomical location. To support a more objective and reproducible approach, this research aims to develop a robust, thoroughly validated kidney abnormality segmentation algorithm, made publicly available for clinical and research use. We employ publicly available training datasets and leverage the state-of-the-art medical image segmentation framework nnU-Net. Validation is conducted using both proprietary and public test datasets, with segmentation performance quantified by Dice coefficient and the 95th percentile Hausdorff distance. Furthermore, we analyze robustness across subgroups based on patient sex, age, CT contrast phases, and tumor histologic subtypes. Our findings demonstrate that our segmentation algorithm, trained exclusively on publicly available data, generalizes effectively to external test sets and outperforms existing state-of-the-art models across all tested datasets. Subgroup analyses reveal consistent high performance, indicating strong robustness and reliability. The developed algorithm and associated code are publicly accessible at https://github.com/DIAGNijmegen/oncology-kidney-abnormality-segmentation.

Felix J. Dorfner, Janis L. Vahldiek, Leonhard Donle et al.

Purpose: To examine whether incorporating anatomical awareness into a deep learning model can improve generalizability and enable prediction of disease progression. Methods: This retrospective multicenter study included conventional pelvic radiographs of 4 different patient cohorts focusing on axial spondyloarthritis (axSpA) collected at university and community hospitals. The first cohort, which consisted of 1483 radiographs, was split into training (n=1261) and validation (n=222) sets. The other cohorts comprising 436, 340, and 163 patients, respectively, were used as independent test datasets. For the second cohort, follow-up data of 311 patients was used to examine progression prediction capabilities. Two neural networks were trained, one on images cropped to the bounding box of the sacroiliac joints (anatomy-aware) and the other one on full radiographs. The performance of the models was compared using the area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, and specificity. Results: On the three test datasets, the standard model achieved AUC scores of 0.853, 0.817, 0.947, with an accuracy of 0.770, 0.724, 0.850. Whereas the anatomy-aware model achieved AUC scores of 0.899, 0.846, 0.957, with an accuracy of 0.821, 0.744, 0.906, respectively. The patients who were identified as high risk by the anatomy aware model had an odds ratio of 2.16 (95% CI: 1.19, 3.86) for having progression of radiographic sacroiliitis within 2 years. Conclusion: Anatomical awareness can improve the generalizability of a deep learning model in detecting radiographic sacroiliitis. The model is published as fully open source alongside this study.

Johannes Moll, Jannik Lübberstedt, Christoph Nuernbergk et al.

Multiple myeloma is managed through sequential lines of therapy over years to decades, with each decision depending on cumulative disease history distributed across dozens to hundreds of heterogeneous clinical documents. Whether LLM-based systems can synthesise this evidence at a level approaching expert agreement has not been established. A retrospective evaluation was conducted on longitudinal clinical records of 811 myeloma patients treated at a tertiary centre (2001-2026), covering 44,962 documents and 1,334,677 laboratory values, with external validation on MIMIC-IV. An agentic reasoning system was compared against single-pass retrieval-augmented generation (RAG), iterative RAG, and full-context input on 469 patient-question pairs from 48 templates at three complexity levels. Reference labels came from double annotation by four oncologists with senior haematologist adjudication. Iterative RAG and full-context input converged on a shared ceiling (75.4% vs 75.8%, p = 1.00). The agentic system reached 79.6% concordance (95% CI 76.4-82.8), exceeding both baselines (+3.8 and +4.2 pp; p = 0.006 and 0.007). Gains rose with question complexity, reaching +9.4 pp on criteria-based synthesis (p = 0.032), and with record length, reaching +13.5 pp in the top decile (n = 10). The system error rate (12.2%) was comparable to expert disagreement (13.6%), but severity was inverted: 57.8% of system errors were clinically significant versus 18.8% of expert disagreements. Agentic reasoning was the only approach to exceed the shared ceiling, with gains concentrated on the most complex questions and longest records. The greater clinical consequence of residual system errors indicates that prospective evaluation in routine care is required before these findings translate into patient benefit.

Hartmut Häntze, Lina Xu, Maximilian Rattunde et al.

Computed tomography (CT) segmentation models often contain classes that are not currently supported by magnetic resonance imaging (MRI) segmentation models. In this study, we show that a simple image inversion technique can significantly improve the segmentation quality of CT segmentation models on MRI data. We demonstrate the feasibility for both a general multi-class and a specific renal carcinoma model for segmenting T1-weighted MRI images. Using this technique, we were able to localize and segment clear cell renal cell carcinoma in T1-weighted MRI scans, using a model that was trained on only CT data. Image inversion is straightforward to implement and does not require dedicated graphics processing units, thus providing a quick alternative to complex deep modality-transfer models. Our results demonstrate that existing CT models, including pathology models, might be transferable to the MRI domain with reasonable effort.

Hartmut Häntze, Myrthe Buser, Alessa Hering et al.

Overlap-based metrics such as the Dice Similarity Coefficient (DSC) penalize segmentation errors more heavily in smaller structures. As organ size differs by sex, this implies that a segmentation error of equal magnitude may result in lower DSCs in women due to their smaller average organ volumes compared to men. While previous work has examined sex-based differences in models or datasets, no study has yet investigated the potential bias introduced by the DSC itself. This study quantifies sex-based differences of the DSC and the normalized DSC in an idealized setting independent of specific models. We applied equally-sized synthetic errors to manual MRI annotations from 50 participants to ensure sex-based comparability. Even minimal errors (e.g., a 1 mm boundary shift) produced systematic DSC differences between sexes. For small structures, average DSC differences were around 0.03; for medium-sized structures around 0.01. Only large structures (i.e., lungs and liver) were mostly unaffected, with sex-based DSC differences close to zero. These findings underline that fairness studies using the DSC as an evaluation metric should not expect identical scores between men and women, as the metric itself introduces bias. A segmentation model may perform equally well across sexes in terms of error magnitude, even if observed DSC values suggest otherwise. Importantly, our work raises awareness of a previously underexplored source of sex-based differences in segmentation performance. One that arises not from model behavior, but from the metric itself. Recognizing this factor is essential for more accurate and fair evaluations in medical image analysis.