arXiv subjects

Jesper Duemose Nielsen

Publications and source records attributed to Jesper Duemose Nielsen.

3 recordsLinked to original sources

arXiv2026

Uncertainty-Aware Cortical Surface Reconstruction and Spherical Registration for Heterogeneous Brain MRI

Surface-based cortical analysis is useful in many applications as it is a natural way to model the highly folded structure of the cerebral cortex, allowing quantities such as curvature and thickness to be easily calculated. Existing deep learning (DL) methods have focused on 1x1x1 mm3 T1-weighted (T1w) scans, thus replicating classical pipelines. Here we present a neural network that is trained exclusively on synthetic scans with random contrast and resolution. Consequently, it can be applied to almost any kind of magnetic resonance imaging (MRI) scan. In addition, our model provides vertex-wise uncertainty estimates of the predicted surface as well as a spherical registration to fsaverage space. Our model performs on par with other state-of-the-art DL methods on 1x1x1 mm3 T1w scans and outperforms the only other method capable of estimating cortical surfaces from low resolution, non-T1w scans. The predicted uncertainty, moreover, correlates with overall scan quality on low resolution scans and highlights areas of poor surface reconstruction on 1x1x1 mm3 T1w scans, suggesting that it can be used for quality control. Finally, the predicted spherical registrations prove comparable to other DL and classical registration methods. These qualities, when combined with the fast inference time, will provide the ability to analyze large, existing databases of clinical MRI scans, with the potential for finding disease-specific patterns that would otherwise be infeasible in a research setting.

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arXiv2025

End-to-end Cortical Surface Reconstruction from Clinical Magnetic Resonance Images

Surface-based cortical analysis is valuable for a variety of neuroimaging tasks, such as spatial normalization, parcellation, and gray matter (GM) thickness estimation. However, most tools for estimating cortical surfaces work exclusively on scans with at least 1 mm isotropic resolution and are tuned to a specific magnetic resonance (MR) contrast, often T1-weighted (T1w). This precludes application using most clinical MR scans, which are very heterogeneous in terms of contrast and resolution. Here, we use synthetic domain-randomized data to train the first neural network for explicit estimation of cortical surfaces from scans of any contrast and resolution, without retraining. Our method deforms a template mesh to the white matter (WM) surface, which guarantees topological correctness. This mesh is further deformed to estimate the GM surface. We compare our method to recon-all-clinical (RAC), an implicit surface reconstruction method which is currently the only other tool capable of processing heterogeneous clinical MR scans, on ADNI and a large clinical dataset (n=1,332). We show a approximately 50 % reduction in cortical thickness error (from 0.50 to 0.24 mm) with respect to RAC and better recovery of the aging-related cortical thinning patterns detected by FreeSurfer on high-resolution T1w scans. Our method enables fast and accurate surface reconstruction of clinical scans, allowing studies (1) with sample sizes far beyond what is feasible in a research setting, and (2) of clinical populations that are difficult to enroll in research studies. The code is publicly available at https://github.com/simnibs/brainnet.

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arXiv2024

Coupled generator decomposition for fusion of electro- and magnetoencephalography data

Data fusion modeling can identify common features across diverse data sources while accounting for source-specific variability. Here we introduce the concept of a \textit{coupled generator decomposition} and demonstrate how it generalizes sparse principal component analysis (SPCA) for data fusion. Leveraging data from a multisubject, multimodal (electro- and magnetoencephalography (EEG and MEG)) neuroimaging experiment, we demonstrate the efficacy of the framework in identifying common features in response to face perception stimuli, while accommodating modality- and subject-specific variability. Through split-half cross-validation of EEG/MEG trials, we investigate the optimal model order and regularization strengths for models of varying complexity, comparing these to a group-level model assuming shared brain responses to stimuli. Our findings reveal altered $\sim170ms$ fusiform face area activation for scrambled faces, as opposed to real faces, particularly evident in the multimodal, multisubject model. Model parameters were inferred using stochastic optimization in PyTorch, demonstrating comparable performance to conventional quadratic programming inference for SPCA but with considerably faster execution. We provide an easily accessible toolbox for coupled generator decomposition that includes data fusion for SPCA, archetypal analysis and directional archetypal analysis. Overall, our approach offers a promising new avenue for data fusion.

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