SIM: Surface-based fMRI Analysis for Inter-Subject Multimodal Decoding from Movie-Watching Experiments

Current AI frameworks for brain decoding and encoding, typically train and test models within the same datasets. This limits their utility for brain computer interfaces (BCI) or neurofeedback, for which it would be useful to pool experiences across individuals to better simulate stimuli not sampled during training. A key obstacle to model generalisation is the degree of variability of inter-subject cortical organisation, which makes it difficult to align or compare cortical signals across participants. In this paper we address this through the use of surface vision transformers, which build a generalisable model of cortical functional dynamics, through encoding the topography of cortical networks and their interactions as a moving image across a surface. This is then combined with tri-modal self-supervised contrastive (CLIP) alignment of audio, video, and fMRI modalities to enable the retrieval of visual and auditory stimuli from patterns of cortical activity (and vice-versa). We validate our approach on 7T task-fMRI data from 174 healthy participants engaged in the movie-watching experiment from the Human Connectome Project (HCP). Results show that it is possible to detect which movie clips an individual is watching purely from their brain activity, even for individuals and movies not seen during training. Further analysis of attention maps reveals that our model captures individual patterns of brain activity that reflect semantic and visual systems. This opens the door to future personalised simulations of brain function. Code & pre-trained models will be made available at https://github.com/metrics-lab/sim, processed data for training will be available upon request at https://gin.g-node.org/Sdahan30/sim.

PARASIDE: An Automatic Paranasal Sinus Segmentation and Structure Analysis Tool for MRI

Chronic rhinosinusitis (CRS) is a common and persistent sinus imflammation that affects 5 - 12\% of the general population. It significantly impacts quality of life and is often difficult to assess due to its subjective nature in clinical evaluation. We introduce PARASIDE, an automatic tool for segmenting air and soft tissue volumes of the structures of the sinus maxillaris, frontalis, sphenodalis and ethmoidalis in T1 MRI. By utilizing that segmentation, we can quantify feature relations that have been observed only manually and subjectively before. We performed an exemplary study and showed both volume and intensity relations between structures and radiology reports. While the soft tissue segmentation is good, the automated annotations of the air volumes are excellent. The average intensity over air structures are consistently below those of the soft tissues, close to perfect separability. Healthy subjects exhibit lower soft tissue volumes and lower intensities. Our developed system is the first automated whole nasal segmentation of 16 structures, and capable of calculating medical relevant features such as the Lund-Mackay score.

Deformable Image Registration of Dark-Field Chest Radiographs for Local Lung Signal Change Assessment

Dark-field radiography of the human chest has been demonstrated to have promising potential for the analysis of the lung microstructure and the diagnosis of respiratory diseases. However, previous studies of dark-field chest radiographs evaluated the lung signal only in the inspiratory breathing state. Our work aims to add a new perspective to these previous assessments by locally comparing dark-field lung information between different respiratory states. To this end, we discuss suitable image registration methods for dark-field chest radiographs to enable consistent spatial alignment of the lung in distinct breathing states. Utilizing full inspiration and expiration scans from a clinical chronic obstructive pulmonary disease study, we assess the performance of the proposed registration framework and outline applicable evaluation approaches. Our regional characterization of lung dark-field signal changes between the breathing states provides a proof-of-principle that dynamic radiography-based lung function assessment approaches may benefit from considering registered dark-field images in addition to standard plain chest radiographs.

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

TimeFlow: Longitudinal Brain Image Registration and Aging Progression Analysis

Predicting future brain states is crucial for understanding healthy aging and neurodegenerative diseases. Longitudinal brain MRI registration, a cornerstone for such analyses, has long been limited by its inability to forecast future developments, reliance on extensive, dense longitudinal data, and the need to balance registration accuracy with temporal smoothness. In this work, we present \emph{TimeFlow}, a novel framework for longitudinal brain MRI registration that overcomes all these challenges. Leveraging a U-Net architecture with temporal conditioning inspired by diffusion models, TimeFlow enables accurate longitudinal registration and facilitates prospective analyses through future image prediction. Unlike traditional methods that depend on explicit smoothness regularizers and dense sequential data, TimeFlow achieves temporal consistency and continuity without these constraints. Experimental results highlight its superior performance in both future timepoint prediction and registration accuracy compared to state-of-the-art methods. Additionally, TimeFlow supports novel biological brain aging analyses, effectively differentiating neurodegenerative conditions from healthy aging. It eliminates the need for segmentation, thereby avoiding the challenges of non-trivial annotation and inconsistent segmentation errors. TimeFlow paves the way for accurate, data-efficient, and annotation-free prospective analyses of brain aging and chronic diseases.

Efficient Deep Learning-based Forward Solvers for Brain Tumor Growth Models

Glioblastoma, a highly aggressive brain tumor, poses major challenges due to its poor prognosis and high morbidity rates. Partial differential equation-based models offer promising potential to enhance therapeutic outcomes by simulating patient-specific tumor behavior for improved radiotherapy planning. However, model calibration remains a bottleneck due to the high computational demands of optimization methods like Monte Carlo sampling and evolutionary algorithms. To address this, we recently introduced an approach leveraging a neural forward solver with gradient-based optimization to significantly reduce calibration time. This approach requires a highly accurate and fully differentiable forward model. We investigate multiple architectures, including (i) an enhanced TumorSurrogate, (ii) a modified nnU-Net, and (iii) a 3D Vision Transformer (ViT). The optimized TumorSurrogate achieved the best overall results, excelling in both tumor outline matching and voxel-level prediction of tumor cell concentration. It halved the MSE relative to the baseline model and achieved the highest Dice score across all tumor cell concentration thresholds. Our study demonstrates significant enhancement in forward solver performance and outlines important future research directions.

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%.

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.

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.

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.