Magnetic resonance imaging (MRI)-guided radiotherapy (MRIgRT) integrates MRI with linear accelerators (MRI-linacs), enabling real-time motion management based on temporally resolved 2D MRI (cine-MRI). Current systems rely on template matching or deformable image registration for radiotherapy target (typically the gross tumor volume) localization, which allows beam gating. Further advances in localization could support more precise and efficient delivery methods. https://trackrad2025.grand-challenge.org/ was organized to provide a common dataset to benchmark algorithms for MRIgRT target tracking in 2D+t cine-MRI. Participants propagated target segmentation masks from an initialization frame across subsequent frames. The dataset comprised sagittal cine-MRI scans of 585 cancer patients undergoing radiotherapy at 0.35 T and 1.5 T MRI-linacs at six different institutions, with expert-annotated targets in 108 sequences. Target sites included the thorax (179 cases), abdomen (266 cases), and pelvis (140 cases). A total of 477 unlabeled and 50 labeled cases were provided for training purposes, 58 cases were kept private for preliminary testing (8) and final evaluation (50). The algorithms submitted by participants were executed on the challenge platform and assessed using metrics in three categories: geometric accuracy, surrogate dose accuracy and execution speed. Rankings were derived via a Rank-Then-Mean scheme. TrackRAD2025 attracted 148 registrations from 28 countries, 100 preliminary submissions and 24 final submissions from 14 teams. The top five methods achieved mean Dice similarity coefficients >0.87 and Euclidean center distances <2.1 mm, comparable to interobserver variability. Leading top five solutions featured foundation models with (4) or without (1) finetuning. Field strength had minimal effect on performance and tracking worked better for the pelvis with reduced motion amplitude compared to the thorax and abdomen cases, which achieved equivalent performance. TrackRAD2025 established a benchmark for MRIgRT tracking on multi-institutional cine-MRI data, highlighting foundation models as promising for clinical translation.

Johannes Moll, Louisa Fay, Asfandyar Azhar, Sophie Ostmeier, Sergios Gatidis, Tim C. Lueth, Curtis Langlotz, Jean-Benoit Delbrouck. Proceedings of the 2025 Conference on Empirical Methods in Natural Language Processing. 2025.

OBJECTIVE: Brief hospital course (BHC) summaries are clinical documents that summarize a patient's hospital stay. While large language models (LLMs) depict remarkable capabilities in automating real-world tasks, their capabilities for healthcare applications such as synthesizing BHCs from clinical notes have not been shown. We introduce a novel preprocessed dataset, the MIMIC-IV-BHC, encapsulating clinical note and BHC pairs to adapt LLMs for BHC synthesis. Furthermore, we introduce a benchmark of the summarization performance of 2 general-purpose LLMs and 3 healthcare-adapted LLMs. MATERIALS AND METHODS: Using clinical notes as input, we apply prompting-based (using in-context learning) and fine-tuning-based adaptation strategies to 3 open-source LLMs (Clinical-T5-Large, Llama2-13B, and FLAN-UL2) and 2 proprietary LLMs (Generative Pre-trained Transformer [GPT]-3.5 and GPT-4). We evaluate these LLMs across multiple context-length inputs using natural language similarity metrics. We further conduct a clinical study with 5 clinicians, comparing clinician-written and LLM-generated BHCs across 30 samples, focusing on their potential to enhance clinical decision-making through improved summary quality. We compare reader preferences for the original and LLM-generated summary using Wilcoxon signed-rank tests. We further request optional qualitative feedback from clinicians to gain deeper insights into their preferences, and we present the frequency of common themes arising from these comments. RESULTS: The Llama2-13B fine-tuned LLM outperforms other domain-adapted models given quantitative evaluation metrics of Bilingual Evaluation Understudy (BLEU) and Bidirectional Encoder Representations from Transformers (BERT)-Score. GPT-4 with in-context learning shows more robustness to increasing context lengths of clinical note inputs than fine-tuned Llama2-13B. Despite comparable quantitative metrics, the reader study depicts a significant preference for summaries generated by GPT-4 with in-context learning compared to both Llama2-13B fine-tuned summaries and the original summaries (P<.001), highlighting the need for qualitative clinical evaluation. DISCUSSION AND CONCLUSION: We release a foundational clinically relevant dataset, the MIMIC-IV-BHC, and present an open-source benchmark of LLM performance in BHC synthesis from clinical notes. We observe high-quality summarization performance for both in-context proprietary and fine-tuned open-source LLMs using both quantitative metrics and a qualitative clinical reader study. Our research effectively integrates elements from the data assimilation pipeline: our methods use (1) clinical data sources to integrate, (2) data translation, and (3) knowledge creation, while our evaluation strategy paves the way for (4) deployment.

We propose a self-supervised feature learning assisted reconstruction (SSFL-Recon) framework for MRI reconstruction to address the limitation of existing supervised learning methods. Although recent deep learning-based methods have shown promising performance in MRI reconstruction, most require fully-sampled images for supervised learning, which is challenging in practice considering long acquisition times under respiratory or organ motion. Moreover, nearly all fully-sampled datasets are obtained from conventional reconstruction of mildly accelerated datasets, thus potentially biasing the achievable performance. The numerous undersampled datasets with different accelerations in clinical practice, hence, remain underutilized. To address these issues, we first train a self-supervised feature extractor on undersampled images to learn sampling-insensitive features. The pre-learned features are subsequently embedded in the self-supervised reconstruction network to assist in removing artifacts. Experiments were conducted retrospectively on an in-house 2D cardiac Cine dataset, including 91 cardiovascular patients and 38 healthy subjects. The results demonstrate that the proposed SSFL-Recon framework outperforms existing self-supervised MRI reconstruction methods and even exhibits comparable or better performance to supervised learning up to ${16}\times $ retrospective undersampling. The feature learning strategy can effectively extract global representations, which have proven beneficial in removing artifacts and increasing generalization ability during reconstruction.

The ability of large language models (LLMs) to follow natural language instructions with human-level fluency suggests many opportunities in healthcare to reduce administrative burden and improve quality of care. However, evaluating LLMs on realistic text generation tasks for healthcare remains challenging. Existing question answering datasets for electronic health record (EHR) data fail to capture the complexity of information needs and documentation burdens experienced by clinicians. To address these challenges, we introduce MedAlign, a benchmark dataset of 983 natural language instructions for EHR data. MedAlign is curated by 15 clinicians (7 specialities), includes clinician-written reference responses for 303 instructions, and provides 276 longitudinal EHRs for grounding instruction-response pairs. We used MedAlign to evaluate 6 general domain LLMs, having clinicians rank the accuracy and quality of each LLM response. We found high error rates, ranging from 35% (GPT-4) to 68% (MPT-7B-Instruct), and 8.3% drop in accuracy moving from 32k to 2k context lengths for GPT-4. Finally, we report correlations between clinician rankings and automated natural language generation metrics as a way to rank LLMs without human review. MedAlign is provided under a research data use agreement to enable LLM evaluations on tasks aligned with clinician needs and preferences.

Age plays an important role in shaping medical decisions, but the biological changes associated with aging do not solely depend on the chronological age. Genetics, lifestyle, and environment cause variations in age-related characteristics, even within the same chronological age group. Biological age (BA) was introduced to better capture an individual’s actual aging process, although its imprecise definition remains a challenge. Organ systems can age at different rates, necessitating organ-specific BA evaluation. To our knowledge, there have been no studies assessing age regionally across multiple organ systems. These age estimations, reflecting various body parts, enable a comprehensive patient-based analysis. We conducted brain, heart, kidney, liver, spleen, pancreas, and retinal fundus age estimations using MRI and OCT scans in 40,000 subjects of the UK Biobank with an uncertainty-aware ResNet-based network. Our results demonstrate the feasibility of organ-specific age estimation with cross-organ correlations of age-related changes. We achieve a mean age difference between predicted and chronological age of 2.72 years across all organs and an averaged Pearson correlation coefficient of 0.87.

Accurate motion estimation at high acceleration factors enables rapid motion-compensated reconstruction in Magnetic Resonance Imaging (MRI) without compromising the diagnostic image quality. In this work, we introduce an attention-aware deep learning-based framework that can perform non-rigid pairwise registration for fully sampled and accelerated MRI. We extract local visual representations to build similarity maps between the registered image pairs at multiple resolution levels and additionally leverage long-range contextual information using a transformer-based module to alleviate ambiguities in the presence of artifacts caused by undersampling. We combine local and global dependencies to perform simultaneous coarse and fine motion estimation. The proposed method was evaluated on in-house acquired fully sampled and accelerated data of 101 patients and 62 healthy subjects undergoing cardiac and thoracic MRI. The impact of motion estimation accuracy on the downstream task of motion-compensated reconstruction was analyzed. We demonstrate that our model derives reliable and consistent motion fields across different sampling trajectories (Cartesian and radial) and acceleration factors of up to 16x for cardiac motion and 30x for respiratory motion and achieves superior image quality in motion-compensated reconstruction qualitatively and quantitatively compared to conventional and recent deep learning-based approaches. The code is publicly available at https://github.com/lab-midas/GMARAFT.

Age is an essential factor in modern diagnostic procedures. However, assessment of the true biological age (BA) remains a daunting task due to the lack of reference ground-truth labels. Current BA estimation approaches are either restricted to skeletal images or rely on non-imaging modalities that yield a whole-body BA assessment. However, various organ systems may exhibit different aging characteristics due to lifestyle and genetic factors. In this initial study, we propose a new framework for organ-specific BA estimation utilizing 3D magnetic resonance image (MRI) scans. As a first step, this framework predicts the chronological age (CA) together with the corresponding patient-dependent aleatoric uncertainty. An iterative training algorithm is then utilized to segregate atypical aging patients from the given population based on the predicted uncertainty scores. In this manner, we hypothesize that training a new model on the remaining population should approximate the true BA behavior. We apply the proposed methodology on a brain MRI dataset containing healthy individuals as well as Alzheimer’s patients. We demonstrate the correlation between the predicted BAs and the expected cognitive deterioration in Alzheimer’s patients.

PET imaging is an important tool in clinical diagnostics, especially in oncology as it is able to visualize ongoing metabolic processes, e.g. caused by a tumor. Due to the low spatial resolution, a corresponding CT or MRI scan is normally necessary to gain knowledge about the physiological structures of a patient and especially to perform some computer-aided diagnostics methods, e.g. segmentation of structures of interest. As this transfer of information from CT/MRI to the PET domain is not always feasible, e.g. when the corresponding CT or MRI images are unavailable or corrupted by artifacts, we propose a novel approach to perform organ segmentation on the PET images directly. We utilize a CNN architecture based on a 3D U-Net combined with a convolutional autoencoder and train our model purely on PET images and corresponding ground truth masks. Our resulting Dice scores of 0.88, 0.82 an 0.59 for liver, spleen and spine, respectively, show that standalone PET organ segmentation is generally feasible.

The concept of biological age (BA) - although important in clinical practice - is hard to grasp mainly due to the lack of a clearly defined reference standard. For specific applications, especially in pediatrics, medical image data are used for BA estimation in a routine clinical context. Beyond this young age group, BA estimation is mostly restricted to whole-body assessment using non-imaging indicators such as blood biomarkers, genetic and cellular data. However, various organ systems may exhibit different aging characteristics due to lifestyle and genetic factors. Thus, a whole-body assessment of the BA does not reflect the deviations of aging behavior between organs. To this end, we propose a new imaging-based framework for organ-specific BA estimation. In this initial study we focus mainly on brain MRI. As a first step, we introduce a chronological age (CA) estimation framework using deep convolutional neural networks (Age-Net). We quantitatively assess the performance of this framework in comparison to existing state-of-the-art CA estimation approaches. Furthermore, we expand upon Age-Net with a novel iterative data-cleaning algorithm to segregate atypical-aging patients (BA [Formula: see text] CA) from the given population. We hypothesize that the remaining population should approximate the true BA behavior. We apply the proposed methodology on a brain magnetic resonance image (MRI) dataset containing healthy individuals as well as Alzheimer's patients with different dementia ratings. We demonstrate the correlation between the predicted BAs and the expected cognitive deterioration in Alzheimer's patients. A statistical and visualization-based analysis has provided evidence regarding the potential and current challenges of the proposed methodology.

Physiological motion, such as cardiac and respiratory motion, during Magnetic Resonance (MR) image acquisition can cause image artifacts. Motion correction techniques have been proposed to compensate for these types of motion during thoracic scans, relying on accurate motion estimation from undersampled motion-resolved reconstruction. A particular interest and challenge lie in the derivation of reliable non-rigid motion fields from the undersampled motion-resolved data. Motion estimation is usually formulated in image space via diffusion, parametric-spline, or optical flow methods. However, image-based registration can be impaired by remaining aliasing artifacts due to the undersampled motion-resolved reconstruction. In this work, we describe a formalism to perform non-rigid registration directly in the sampled Fourier space, i.e. k-space. We propose a deep-learning based approach to perform fast and accurate non-rigid registration from the undersampled k-space data. The basic working principle originates from the Local All-Pass (LAP) technique, a recently introduced optical flow-based registration. The proposed LAPNet is compared against traditional and deep learning image-based registrations and tested on fully-sampled and highly-accelerated (with two undersampling strategies) 3D respiratory motion-resolved MR images in a cohort of 40 patients with suspected liver or lung metastases and 25 healthy subjects. The proposed LAPNet provided consistent and superior performance to image-based approaches throughout different sampling trajectories and acceleration factors.

Local deformations in medical modalities are common phenomena due to a multitude of factors such as metallic implants or limited field of views in magnetic resonance imaging (MRI). Completion of the missing or distorted regions is of special interest for automatic image analysis frameworks to enhance post-processing tasks such as segmentation or classification. In this work, we propose a new generative framework for medical image inpainting, titled ipA-MedGAN. It bypasses the limitations of previous frameworks by enabling inpainting of arbitrary shaped regions without a prior localization of the regions of interest. Thorough qualitative and quantitative comparisons with other inpainting and translational approaches have illustrated the superior performance of the proposed framework for the task of brain MR inpainting.

Numerous factors could lead to partial deteriorations of medical images. For example, metallic implants will lead to localized perturbations in MRI scans. This will affect further post-processing tasks such as attenuation correction in PET/MRI or radiation therapy planning. In this work, we propose the inpainting of medical images via Generative Adversarial Networks (GANs). The proposed framework incorporates two patch-based discriminator networks with additional style and perceptual losses for the inpainting of missing information in realistically detailed and contextually consistent manner. The proposed framework outperformed other natural image inpainting techniques both qualitatively and quantitatively on two different medical modalities.

Magnetic resonance (MR) plays an important role in medical imaging. It can be flexibly tuned towards different applications for deriving a meaningful diagnosis. However, its long acquisition times and flexible parametrization make it on the other hand prone to artifacts which obscure the underlying image content or can be misinterpreted as anatomy. Patient-induced motion artifacts are still one of the major extrinsic factors which degrade image quality. In this work, an automatic reference-free motion artifact detection, including localization and quantification, is proposed which can be used prospectively as quality control (e.g. scan adjustment) or retrospectively as quality control (e.g. supported diagnosis). The detection is achieved via trained convolutional neural networks (CNN). This study focuses on investigating the optimal CNN architecture and required training set composition to derive a general and robust network for MR motion artifact detection. In a volunteer cohort an average accuracy of 91% was achieved.

Combined PET-CT scan is an important diagnostic tool in modern medicine, e.g. for staging or treatment planning in the field of oncology. Especially in small structures, like a tumour, textural variations visible in a PET image are not visually recognizable within a CT scan from the same region. Thus, both modalities are necessary for diagnosis. Since both techniques expose the patient to radiation, it would be desirable to get the same information about metabolic activity contained in the PET image from a CT scan only. To investigate the relationship between both imaging modalities, we propose a machine learning approach to automatically identify regions in a CT scan corresponding to areas with high FDG uptakes in a PET image.

Automated organ segmentation is a prerequisite for efficient analysis of MR data in large cohorts with thousands of participants. The feasibility and generalizability of previously proposed methods has mostly been demonstrated in smaller cohorts. The aim of this work is to implement and validate automated semantic 3D segmentation of liver and spleen on multi-contrast MR data of the body trunk which were acquired in a large epidemiological imaging study with the objective to provide a robust and general setup in a setting of limited training data. Liver and spleen were manually segmented in 173 MR images by an experienced radiologist, providing labeled ground-truth. Varying amount of training datasets were randomly chosen to train a convolutional neural network (CNN)-based segmentation with 4-fold patient-leave-out cross-validation and compared against a Random Forest (RF)-based segmentation. Validation amongst participants revealed high accuracies of 99.7%/99.9% for liver/spleen-segmentation with superiority of CNN to RF. In conclusion, automated semantic organ segmentation is feasible in a robust and general setup.

In medical imaging, the acquired images are usually analyzed by a human observer and rated with respect to a diagnostic question. However, this procedure is time-demanding and expensive. Further more, the lack of a reference image makes this task challenging. In order to support the human observer in assessing image quality and to ensure an objective evaluation, we extend in this paper our previous no-reference magnetic resonance (MR) image quality assessment system with an active learning loop to reduce the amount of necessary labeled training data. We employ two different active learning query strategies based on uncertainty sampling. Since the classification task is performed on 2D image slices, but the human observer labels complete 3D image volumes, we present a method to select representative 3D images instead of independant 2D image slices. The performance is evaluated on in-vivo MR image data.

A Cartesian subsampling scheme is proposed incorporating the idea of PF acquisition and variable-density Poisson Disc (vdPD) subsampling by redistributing the sampling space onto a smaller region aiming to increase k-space sampling density for a given acceleration factor. Especially the normally sparse sampled high-frequency components benefit from this sampling redistribution, leading to improved edge delineation. The prospective subsampled and compacted k-space can be reconstructed by a seamless combination of a CS-algorithm with a Hermitian symmetry constraint accounting for the missing part of the k-space. This subsampling and reconstruction scheme is called Compressed Sensing Partial Subsampling (ESPReSSo) and was tested on in-vivo abdominal MRI datasets. Different reconstruction methods and regularizations are investigated and analyzed via global (intensity-based) and local (region-of-interest and line evaluation) image metrics, to conclude a clinical feasible setup. Results substantiate that ESPReSSo can provide improved edge delineation and regional homogeneity for multidimensional and multi-coil MRI datasets and is therefore useful in applications depending on well-defined tissue boundaries, such as image registration and segmentation or detection of small lesions in clinical diagnostics.