arXiv subjects

Daniel Rueckert

Publications and source records attributed to Daniel Rueckert.

At least 145 records · Page 8Linked to original sources

arXiv2025

PISCO: Self-Supervised k-Space Regularization for Improved Neural Implicit k-Space Representations of Dynamic MRI

Neural implicit k-space representations (NIK) have shown promising results for dynamic magnetic resonance imaging (MRI) at high temporal resolutions. Yet, reducing acquisition time, and thereby available training data, results in severe performance drops due to overfitting. To address this, we introduce a novel self-supervised k-space loss function $\mathcal{L}_\mathrm{PISCO}$, applicable for regularization of NIK-based reconstructions. The proposed loss function is based on the concept of parallel imaging-inspired self-consistency (PISCO), enforcing a consistent global k-space neighborhood relationship without requiring additional data. Quantitative and qualitative evaluations on static and dynamic MR reconstructions show that integrating PISCO significantly improves NIK representations. Particularly for high acceleration factors (R$\geq$54), NIK with PISCO achieves superior spatio-temporal reconstruction quality compared to state-of-the-art methods. Furthermore, an extensive analysis of the loss assumptions and stability shows PISCO's potential as versatile self-supervised k-space loss function for further applications and architectures. Code is available at: https://github.com/compai-lab/2025-pisco-spieker

eess.IV↗

arXiv2025

Unlocking the diagnostic potential of electrocardiograms through information transfer from cardiac magnetic resonance imaging

Cardiovascular diseases (CVD) can be diagnosed using various diagnostic modalities. The electrocardiogram (ECG) is a cost-effective and widely available diagnostic aid that provides functional information of the heart. However, its ability to classify and spatially localise CVD is limited. In contrast, cardiac magnetic resonance (CMR) imaging provides detailed structural information of the heart and thus enables evidence-based diagnosis of CVD, but long scan times and high costs limit its use in clinical routine. In this work, we present a deep learning strategy for cost-effective and comprehensive cardiac screening solely from ECG. Our approach combines multimodal contrastive learning with masked data modelling to transfer domain-specific information from CMR imaging to ECG representations. In extensive experiments using data from 40,044 UK Biobank subjects, we demonstrate the utility and generalisability of our method for subject-specific risk prediction of CVD and the prediction of cardiac phenotypes using only ECG data. Specifically, our novel multimodal pre-training paradigm improves performance by up to 12.19 % for risk prediction and 27.59 % for phenotype prediction. In a qualitative analysis, we demonstrate that our learned ECG representations incorporate information from CMR image regions of interest. Our entire pipeline is publicly available at https://github.com/oetu/MMCL-ECG-CMR.

eess.SP↗

arXiv2024

From Model Based to Learned Regularization in Medical Image Registration: A Comprehensive Review

Image registration is fundamental in medical imaging applications, such as disease progression analysis or radiation therapy planning. The primary objective of image registration is to precisely capture the deformation between two or more images, typically achieved by minimizing an optimization problem. Due to its inherent ill-posedness, regularization is a key component in driving the solution toward anatomically meaningful deformations. A wide range of regularization methods has been proposed for both conventional and deep learning-based registration. However, the appropriate application of regularization techniques often depends on the specific registration problem, and no one-fits-all method exists. Despite its importance, regularization is often overlooked or addressed with default approaches, assuming existing methods are sufficient. A comprehensive and structured review remains missing. This review addresses this gap by introducing a novel taxonomy that systematically categorizes the diverse range of proposed regularization methods. It highlights the emerging field of learned regularization, which leverages data-driven techniques to automatically derive deformation properties from the data. Moreover, this review examines the transfer of regularization methods from conventional to learning-based registration, identifies open challenges, and outlines future research directions. By emphasizing the critical role of regularization in image registration, we hope to inspire the research community to reconsider regularization strategies in modern registration algorithms and to explore this rapidly evolving field further.

eess.IV↗

arXiv2024

Self-Supervised Radiograph Anatomical Region Classification -- How Clean Is Your Real-World Data?

Modern deep learning-based clinical imaging workflows rely on accurate labels of the examined anatomical region. Knowing the anatomical region is required to select applicable downstream models and to effectively generate cohorts of high quality data for future medical and machine learning research efforts. However, this information may not be available in externally sourced data or generally contain data entry errors. To address this problem, we show the effectiveness of self-supervised methods such as SimCLR and BYOL as well as supervised contrastive deep learning methods in assigning one of 14 anatomical region classes in our in-house dataset of 48,434 skeletal radiographs. We achieve a strong linear evaluation accuracy of 96.6% with a single model and 97.7% using an ensemble approach. Furthermore, only a few labeled instances (1% of the training set) suffice to achieve an accuracy of 92.2%, enabling usage in low-label and thus low-resource scenarios. Our model can be used to correct data entry mistakes: a follow-up analysis of the test set errors of our best-performing single model by an expert radiologist identified 35% incorrect labels and 11% out-of-domain images. When accounted for, the radiograph anatomical region labelling performance increased -- without and with an ensemble, respectively -- to a theoretical accuracy of 98.0% and 98.8%.

cs.CV↗

arXiv2024

Pitfalls of topology-aware image segmentation

Topological correctness, i.e., the preservation of structural integrity and specific characteristics of shape, is a fundamental requirement for medical imaging tasks, such as neuron or vessel segmentation. Despite the recent surge in topology-aware methods addressing this challenge, their real-world applicability is hindered by flawed benchmarking practices. In this paper, we identify critical pitfalls in model evaluation that include inadequate connectivity choices, overlooked topological artifacts in ground truth annotations, and inappropriate use of evaluation metrics. Through detailed empirical analysis, we uncover these issues' profound impact on the evaluation and ranking of segmentation methods. Drawing from our findings, we propose a set of actionable recommendations to establish fair and robust evaluation standards for topology-aware medical image segmentation methods.

cs.CV↗

arXiv2024

DCRA-Net: Attention-Enabled Reconstruction Model for Dynamic Fetal Cardiac MRI

Dynamic fetal heart magnetic resonance imaging (MRI) presents unique challenges due to the fast heart rate of the fetus compared to adult subjects and uncontrolled fetal motion. This requires high temporal and spatial resolutions over a large field of view, in order to encompass surrounding maternal anatomy. In this work, we introduce Dynamic Cardiac Reconstruction Attention Network (DCRA-Net) - a novel deep learning model that employs attention mechanisms in spatial and temporal domains and temporal frequency representation of data to reconstruct the dynamics of the fetal heart from highly accelerated free-running (non-gated) MRI acquisitions. DCRA-Net was trained on retrospectively undersampled complex-valued cardiac MRIs from 42 fetal subjects and separately from 153 adult subjects, and evaluated on data from 14 fetal and 39 adult subjects respectively. Its performance was compared to L+S and k-GIN methods in both fetal and adult cases for an undersampling factor of 8x. The proposed network performed better than the comparators for both fetal and adult data, for both regular lattice and centrally weighted random undersampling. Aliased signals due to the undersampling were comprehensively resolved, and both the spatial details of the heart and its temporal dynamics were recovered with high fidelity. The highest performance was achieved when using lattice undersampling, data consistency and temporal frequency representation, yielding PSNR of 38 for fetal and 35 for adult cases. Our method is publicly available at https://github.com/denproc/DCRA-Net.

eess.IV↗

arXiv2024

Subspace Implicit Neural Representations for Real-Time Cardiac Cine MR Imaging

Conventional cardiac cine MRI methods rely on retrospective gating, which limits temporal resolution and the ability to capture continuous cardiac dynamics, particularly in patients with arrhythmias and beat-to-beat variations. To address these challenges, we propose a reconstruction framework based on subspace implicit neural representations for real-time cardiac cine MRI of continuously sampled radial data. This approach employs two multilayer perceptrons to learn spatial and temporal subspace bases, leveraging the low-rank properties of cardiac cine MRI. Initialized with low-resolution reconstructions, the networks are fine-tuned using spoke-specific loss functions to recover spatial details and temporal fidelity. Our method directly utilizes the continuously sampled radial k-space spokes during training, thereby eliminating the need for binning and non-uniform FFT. This approach achieves superior spatial and temporal image quality compared to conventional binned methods at the acceleration rate of 10 and 20, demonstrating potential for high-resolution imaging of dynamic cardiac events and enhancing diagnostic capability.

eess.IV↗

arXiv2024

Neural Network Surrogate and Projected Gradient Descent for Fast and Reliable Finite Element Model Calibration: a Case Study on an Intervertebral Disc

Accurate calibration of finite element (FE) models is essential across various biomechanical applications, including human intervertebral discs (IVDs), to ensure their reliability and use in diagnosing and planning treatments. However, traditional calibration methods are computationally intensive, requiring iterative, derivative-free optimization algorithms that often take days to converge. This study addresses these challenges by introducing a novel, efficient, and effective calibration method demonstrated on a human L4-L5 IVD FE model as a case study using a neural network (NN) surrogate. The NN surrogate predicts simulation outcomes with high accuracy, outperforming other machine learning models, and significantly reduces the computational cost associated with traditional FE simulations. Next, a Projected Gradient Descent (PGD) approach guided by gradients of the NN surrogate is proposed to efficiently calibrate FE models. Our method explicitly enforces feasibility with a projection step, thus maintaining material bounds throughout the optimization process. The proposed method is evaluated against SOTA Genetic Algorithm and inverse model baselines on synthetic and in vitro experimental datasets. Our approach demonstrates superior performance on synthetic data, achieving an MAE of 0.06 compared to the baselines' MAE of 0.18 and 0.54, respectively. On experimental specimens, our method outperforms the baseline in 5 out of 6 cases. While our approach requires initial dataset generation and surrogate training, these steps are performed only once, and the actual calibration takes under three seconds. In contrast, traditional calibration time scales linearly with the number of specimens, taking up to 8 days in the worst-case. Such efficiency paves the way for applying more complex FE models, potentially extending beyond IVDs, and enabling accurate patient-specific simulations.

cs.LG↗

arXiv2024

Cross-domain and Cross-dimension Learning for Image-to-Graph Transformers

Direct image-to-graph transformation is a challenging task that involves solving object detection and relationship prediction in a single model. Due to this task's complexity, large training datasets are rare in many domains, making the training of deep-learning methods challenging. This data sparsity necessitates transfer learning strategies akin to the state-of-the-art in general computer vision. In this work, we introduce a set of methods enabling cross-domain and cross-dimension learning for image-to-graph transformers. We propose (1) a regularized edge sampling loss to effectively learn object relations in multiple domains with different numbers of edges, (2) a domain adaptation framework for image-to-graph transformers aligning image- and graph-level features from different domains, and (3) a projection function that allows using 2D data for training 3D transformers. We demonstrate our method's utility in cross-domain and cross-dimension experiments, where we utilize labeled data from 2D road networks for simultaneous learning in vastly different target domains. Our method consistently outperforms standard transfer learning and self-supervised pretraining on challenging benchmarks, such as retinal or whole-brain vessel graph extraction.

cs.CV↗

arXiv2024

Improved Localized Machine Unlearning Through the Lens of Memorization

Machine unlearning refers to removing the influence of a specified subset of training data from a machine learning model, efficiently, after it has already been trained. This is important for key applications, including making the model more accurate by removing outdated, mislabeled, or poisoned data. In this work, we study localized unlearning, where the unlearning algorithm operates on a (small) identified subset of parameters. Drawing inspiration from the memorization literature, we propose an improved localization strategy that yields strong results when paired with existing unlearning algorithms. We also propose a new unlearning algorithm, Deletion by Example Localization (DEL), that resets the parameters deemed-to-be most critical according to our localization strategy, and then finetunes them. Our extensive experiments on different datasets, forget sets and metrics reveal that DEL sets a new state-of-the-art for unlearning metrics, against both localized and full-parameter methods, while modifying a small subset of parameters, and outperforms the state-of-the-art localized unlearning in terms of test accuracy too.

cs.LG↗

arXiv2024

Using UK Biobank data to establish population-specific atlases from whole body MRI

Reliable reference data in medical imaging is largely unavailable. Developing tools that allow for the comparison of individual patient data to reference data has a high potential to improve diagnostic imaging. Population atlases are a commonly used tool in medical imaging to facilitate this. Constructing such atlases becomes particularly challenging when working with highly heterogeneous datasets, such as whole-body images, which contain significant anatomical variations. In this work, we propose a pipeline for generating a standardised whole-body atlas for a highly heterogeneous population by partitioning the population into anatomically meaningful subgroups. Using magnetic resonance images from the UK Biobank dataset, we create six whole-body atlases representing a healthy population average. We furthermore unbias them, and this way obtain a realistic representation of the population. In addition to the anatomical atlases, we generate probabilistic atlases that capture the distributions of abdominal fat (visceral and subcutaneous) and five abdominal organs across the population (liver, spleen, pancreas, left and right kidneys). Our pipeline effectively generates high-quality, realistic whole-body atlases with clinical applicability. The probabilistic atlases show differences in fat distribution between subjects with medical conditions such as diabetes and cardiovascular diseases and healthy subjects in the atlas space. With this work, we make the constructed anatomical and label atlases publically available, with the expectation that they will support medical research involving whole-body MR images.

eess.IV↗

arXiv2024

Atlas-Based Interpretable Age Prediction In Whole-Body MR Images

Age prediction is an important part of medical assessments and research. It can aid in detecting diseases as well as abnormal ageing by highlighting potential discrepancies between chronological and biological age. To improve understanding of age-related changes in various body parts, we investigate the ageing of the human body on a large scale by using whole-body 3D images. We utilise the Grad-CAM method to determine the body areas most predictive of a person's age. In order to expand our analysis beyond individual subjects, we employ registration techniques to generate population-wide importance maps that show the most predictive areas in the body for a whole cohort of subjects. We show that the investigation of the full 3D volume of the whole body and the population-wide analysis can give important insights into which body parts play the most important roles in predicting a person's age. Our findings reveal three primary areas of interest: the spine, the autochthonous back muscles, and the cardiac region, which exhibits the highest importance. Finally, we investigate differences between subjects that show accelerated and decelerated ageing.

eess.IV↗

arXiv2024

The Developing Human Connectome Project: A Fast Deep Learning-based Pipeline for Neonatal Cortical Surface Reconstruction

The Developing Human Connectome Project (dHCP) aims to explore developmental patterns of the human brain during the perinatal period. An automated processing pipeline has been developed to extract high-quality cortical surfaces from structural brain magnetic resonance (MR) images for the dHCP neonatal dataset. However, the current implementation of the pipeline requires more than 6.5 hours to process a single MRI scan, making it expensive for large-scale neuroimaging studies. In this paper, we propose a fast deep learning (DL) based pipeline for dHCP neonatal cortical surface reconstruction, incorporating DL-based brain extraction, cortical surface reconstruction and spherical projection, as well as GPU-accelerated cortical surface inflation and cortical feature estimation. We introduce a multiscale deformation network to learn diffeomorphic cortical surface reconstruction end-to-end from T2-weighted brain MRI. A fast unsupervised spherical mapping approach is integrated to minimize metric distortions between cortical surfaces and projected spheres. The entire workflow of our DL-based dHCP pipeline completes within only 24 seconds on a modern GPU, which is nearly 1000 times faster than the original dHCP pipeline. The qualitative assessment demonstrates that for 82.5% of the test samples, the cortical surfaces reconstructed by our DL-based pipeline achieve superior (54.2%) or equal (28.3%) surface quality compared to the original dHCP pipeline.

eess.IV↗

arXiv2024

MRSegmentator: Multi-Modality Segmentation of 40 Classes in MRI and CT

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.

eess.IV↗

arXiv2024

A Learnable Prior Improves Inverse Tumor Growth Modeling

Biophysical modeling, particularly involving partial differential equations (PDEs), offers significant potential for tailoring disease treatment protocols to individual patients. However, the inverse problem-solving aspect of these models presents a substantial challenge, either due to the high computational requirements of model-based approaches or the limited robustness of deep learning (DL) methods. We propose a novel framework that leverages the unique strengths of both approaches in a synergistic manner. Our method incorporates a DL ensemble for initial parameter estimation, facilitating efficient downstream evolutionary sampling initialized with this DL-based prior. We showcase the effectiveness of integrating a rapid deep-learning algorithm with a high-precision evolution strategy in estimating brain tumor cell concentrations from magnetic resonance images. The DL-Prior plays a pivotal role, significantly constraining the effective sampling-parameter space. This reduction results in a fivefold convergence acceleration and a Dice-score of 95%.

physics.med-ph↗

arXiv2024

How Low Can You Go? Surfacing Prototypical In-Distribution Samples for Unsupervised Anomaly Detection

Unsupervised anomaly detection (UAD) alleviates large labeling efforts by training exclusively on unlabeled in-distribution data and detecting outliers as anomalies. Generally, the assumption prevails that large training datasets allow the training of higher-performing UAD models. However, in this work, we show that UAD with extremely few training samples can already match -- and in some cases even surpass -- the performance of training with the whole training dataset. Building upon this finding, we propose an unsupervised method to reliably identify prototypical samples to further boost UAD performance. We demonstrate the utility of our method on seven different established UAD benchmarks from computer vision, industrial defect detection, and medicine. With just 25 selected samples, we even exceed the performance of full training in $25/67$ categories in these benchmarks. Additionally, we show that the prototypical in-distribution samples identified by our proposed method generalize well across models and datasets and that observing their sample selection criteria allows for a successful manual selection of small subsets of high-performing samples. Our code is available at https://anonymous.4open.science/r/uad_prototypical_samples/

cs.CV↗

arXiv2024

Spatiotemporal Representation Learning for Short and Long Medical Image Time Series

Analyzing temporal developments is crucial for the accurate prognosis of many medical conditions. Temporal changes that occur over short time scales are key to assessing the health of physiological functions, such as the cardiac cycle. Moreover, tracking longer term developments that occur over months or years in evolving processes, such as age-related macular degeneration (AMD), is essential for accurate prognosis. Despite the importance of both short and long term analysis to clinical decision making, they remain understudied in medical deep learning. State of the art methods for spatiotemporal representation learning, developed for short natural videos, prioritize the detection of temporal constants rather than temporal developments. Moreover, they do not account for varying time intervals between acquisitions, which are essential for contextualizing observed changes. To address these issues, we propose two approaches. First, we combine clip-level contrastive learning with a novel temporal embedding to adapt to irregular time series. Second, we propose masking and predicting latent frame representations of the temporal sequence. Our two approaches outperform all prior methods on temporally-dependent tasks including cardiac output estimation and three prognostic AMD tasks. Overall, this enables the automated analysis of temporal patterns which are typically overlooked in applications of deep learning to medicine.

cs.CV↗

arXiv2024

Highly efficient non-rigid registration in k-space with application to cardiac Magnetic Resonance Imaging

In Magnetic Resonance Imaging (MRI), high temporal-resolved motion can be useful for image acquisition and reconstruction, MR-guided radiotherapy, dynamic contrast-enhancement, flow and perfusion imaging, and functional assessment of motion patterns in cardiovascular, abdominal, peristaltic, fetal, or musculoskeletal imaging. Conventionally, these motion estimates are derived through image-based registration, a particularly challenging task for complex motion patterns and high dynamic resolution. The accelerated scans in such applications result in imaging artifacts that compromise the motion estimation. In this work, we propose a novel self-supervised deep learning-based framework, dubbed the Local-All Pass Attention Network (LAPANet), for non-rigid motion estimation directly from the acquired accelerated Fourier space, i.e. k-space. The proposed approach models non-rigid motion as the cumulative sum of local translational displacements, following the Local All-Pass (LAP) registration technique. LAPANet was evaluated on cardiac motion estimation across various sampling trajectories and acceleration rates. Our results demonstrate superior accuracy compared to prior conventional and deep learning-based registration methods, accommodating as few as 2 lines/frame in a Cartesian trajectory and 3 spokes/frame in a non-Cartesian trajectory. The achieved high temporal resolution (less than 5 ms) for non-rigid motion opens new avenues for motion detection, tracking and correction in dynamic and real-time MRI applications.

eess.IV↗