Lukas T. Rotkopf

Lukas T. Rotkopf, Marco Schlimbach, Julius C. Holzschuh et al.

Purpose: To assess whether breast lesion segmentation can be learned directly from acquired MRI k-space, and whether doing so improves robustness when data are accelerated or noisy. Materials and Methods: This retrospective study used public breast dynamic contrast-enhanced MRI (DCE-MRI) datasets with acquired and synthetic k-space, together with a within-dataset synthetic control. We compared four 3D U-Net variants: a hybrid k-space-to-image model, a native k-space model, and magnitude and complex image-space baselines. Models were evaluated under increasing undersampling and added complex Gaussian k-space noise. The primary outcome was patient-level Dice similarity coefficient under cross-validation, with the hybrid model prespecified as the main comparison against the magnitude image-space baseline. Results: At full sampling, the hybrid and image-space models performed similarly. As acceleration increased, the hybrid model retained substantially more segmentation accuracy and significantly outperformed the magnitude image-space baseline across moderate to high undersampling levels. The same pattern was observed when noise was added directly to k-space: the hybrid model degraded more slowly, whereas the image-space baseline failed under heavier noise. This advantage was reproduced in the within-dataset synthetic control. Feature analysis suggested that the k-space stage and image-space stage played complementary roles, with frequency-domain filtering concentrated before image-domain lesion localization. Conclusion: K-space-aware deep learning improves the robustness of breast lesion segmentation under MRI undersampling and k-space noise, while matching image-space methods at full sampling.

Marco Schlimbach, Moritz Rempe, Jessica Mnischek et al.

Objective. Standard Magnetic Resonance Imaging (MRI) reconstruction pipelines discard phase information captured during acquisition, despite evidence that it encodes tissue properties relevant to tumor diagnosis. Current machine learning approaches inherit this limitation by operating exclusively on reconstructed magnitude images. The aim of this study is to build a generative framework which is capable of jointly modeling magnitude and phase information of complex-valued MRI scans. Approach. The proposed generative framework combines a conditional variational autoencoder, which compresses complex-valued MRI scans into compact latent representations while preserving phase coherence, with a flow-matching-based generative model. Synthetic sample quality is assessed via a real-versus-synthetic classifier and by training downstream classifiers on synthetic data for abnormal tissue detection. Main results. The autoencoder preserves phase coherence above 0.997. Real-versus-synthetic classification yields low AUROC values between 0.50 and 0.66 across all acquisition sequences, indicating generated samples are nearly indistinguishable from real data. In downstream normal-versus-abnormal classification, classifiers trained entirely on synthetic data achieve an AUROC of 0.880, surpassing the real-data baseline of 0.842 on a publicly available dataset (fastMRI). This advantage persists on an independent external test set from a different institution with biopsy-confirmed labels. Significance. The proposed framework demonstrates the feasibility of jointly modeling magnitude and phase information for normal and abnormal complex-valued brain MRI data. Beyond synthetic data generation, it establishes a foundation for the usage of complete brain MRI information in future diagnostic applications and enables systematic investigation of how magnitude and phase jointly encode pathology-specific features.

Maximilian Rokuss, Yannick Kirchhoff, Seval Akbal et al.

In this work, we present LesionLocator, a framework for zero-shot longitudinal lesion tracking and segmentation in 3D medical imaging, establishing the first end-to-end model capable of 4D tracking with dense spatial prompts. Our model leverages an extensive dataset of 23,262 annotated medical scans, as well as synthesized longitudinal data across diverse lesion types. The diversity and scale of our dataset significantly enhances model generalizability to real-world medical imaging challenges and addresses key limitations in longitudinal data availability. LesionLocator outperforms all existing promptable models in lesion segmentation by nearly 10 dice points, reaching human-level performance, and achieves state-of-the-art results in lesion tracking, with superior lesion retrieval and segmentation accuracy. LesionLocator not only sets a new benchmark in universal promptable lesion segmentation and automated longitudinal lesion tracking but also provides the first open-access solution of its kind, releasing our synthetic 4D dataset and model to the community, empowering future advancements in medical imaging. Code is available at: www.github.com/MIC-DKFZ/LesionLocator

Moritz Rempe, Lukas T. Rotkopf, Marco Schlimbach et al.

Deep learning applications in Magnetic Resonance Imaging (MRI) predominantly operate on reconstructed magnitude images, a process that discards phase information and requires computationally expensive transforms. Standard neural network architectures rely on local operations (convolutions or grid-patches) that are ill-suited for the global, non-local nature of raw frequency-domain (k-Space) data. In this work, we propose a novel complex-valued Vision Transformer (kViT) designed to perform classification directly on k-Space data. To bridge the geometric disconnect between current architectures and MRI physics, we introduce a radial k-Space patching strategy that respects the spectral energy distribution of the frequency-domain. Extensive experiments on the fastMRI and in-house datasets demonstrate that our approach achieves classification performance competitive with state-of-the-art image-domain baselines (ResNet, EfficientNet, ViT). Crucially, kViT exhibits superior robustness to high acceleration factors and offers a paradigm shift in computational efficiency, reducing VRAM consumption during training by up to 68$\times$ compared to standard methods. This establishes a pathway for resource-efficient, direct-from-scanner AI analysis.