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GOUHFI: a novel contrast- and resolution-agnostic segmentation tool for Ultra-High Field MRI

Marc-Antoine Fortin, Anne Louise Kristoffersen, Michael Staff Larsen, Laurent Lamalle, Ruediger Stirnberg, Paal Erik Goa

arxiv logopreprintMay 16 2025
Recently, Ultra-High Field MRI (UHF-MRI) has become more available and one of the best tools to study the brain. One common step in quantitative neuroimaging is the brain segmentation. However, the differences between UHF-MRI and 1.5-3T images are such that the automatic segmentation techniques optimized at these field strengths usually produce unsatisfactory segmentation results for UHF images. It has been particularly challenging to perform quantitative analyses as typically done with 1.5-3T data, considerably limiting the potential of UHF-MRI. Hence, we propose a novel Deep Learning (DL)-based segmentation technique called GOUHFI: Generalized and Optimized segmentation tool for Ultra-High Field Images, designed to segment UHF images of various contrasts and resolutions. For training, we used a total of 206 label maps from four datasets acquired at 3T, 7T and 9.4T. In contrast to most DL strategies, we used a previously proposed domain randomization approach, where synthetic images generated from the label maps were used for training a 3D U-Net. GOUHFI was tested on seven different datasets and compared to techniques like FastSurferVINN and CEREBRUM-7T. GOUHFI was able to the segment six contrasts and seven resolutions tested at 3T, 7T and 9.4T. Average Dice-Sorensen Similarity Coefficient (DSC) scores of 0.87, 0.84, 0.91 were computed against the ground truth segmentations at 3T, 7T and 9.4T. Moreover, GOUHFI demonstrated impressive resistance to the typical inhomogeneities observed at UHF-MRI, making it a new powerful segmentation tool that allows to apply the usual quantitative analysis pipelines also at UHF. Ultimately, GOUHFI is a promising new segmentation tool, being the first of its kind proposing a contrast- and resolution-agnostic alternative for UHF-MRI, making it the forthcoming alternative for neuroscientists working with UHF-MRI or even lower field strengths.

Development and validation of clinical-radiomics deep learning model based on MRI for endometrial cancer molecular subtypes classification.

Yue W, Han R, Wang H, Liang X, Zhang H, Li H, Yang Q

pubmed logopapersMay 16 2025
This study aimed to develop and validate a clinical-radiomics deep learning (DL) model based on MRI for endometrial cancer (EC) molecular subtypes classification. This multicenter retrospective study included EC patients undergoing surgery, MRI, and molecular pathology diagnosis across three institutions from January 2020 to March 2024. Patients were divided into training, internal, and external validation cohorts. A total of 386 handcrafted radiomics features were extracted from each MR sequence, and MoCo-v2 was employed for contrastive self-supervised learning to extract 2048 DL features per patient. Feature selection integrated selected features into 12 machine learning methods. Model performance was evaluated with the AUC. A total of 526 patients were included (mean age, 55.01 ± 11.07). The radiomics model and clinical model demonstrated comparable performance across the internal and external validation cohorts, with macro-average AUCs of 0.70 vs 0.69 and 0.70 vs 0.67 (p = 0.51), respectively. The radiomics DL model, compared to the radiomics model, improved AUCs for POLEmut (0.68 vs 0.79), NSMP (0.71 vs 0.74), and p53abn (0.76 vs 0.78) in the internal validation (p = 0.08). The clinical-radiomics DL Model outperformed both the clinical model and radiomics DL model (macro-average AUC = 0.79 vs 0.69 and 0.73, in the internal validation [p = 0.02], 0.74 vs 0.67 and 0.69 in the external validation [p = 0.04]). The clinical-radiomics DL model based on MRI effectively distinguished EC molecular subtypes and demonstrated strong potential, with robust validation across multiple centers. Future research should explore larger datasets to further uncover DL's potential. Our clinical-radiomics DL model based on MRI has the potential to distinguish EC molecular subtypes. This insight aids in guiding clinicians in tailoring individualized treatments for EC patients. Accurate classification of EC molecular subtypes is crucial for prognostic risk assessment. The clinical-radiomics DL model outperformed both the clinical model and the radiomics DL model. The MRI features exhibited better diagnostic performance for POLEmut and p53abn.

Diff-Unfolding: A Model-Based Score Learning Framework for Inverse Problems

Yuanhao Wang, Shirin Shoushtari, Ulugbek S. Kamilov

arxiv logopreprintMay 16 2025
Diffusion models are extensively used for modeling image priors for inverse problems. We introduce \emph{Diff-Unfolding}, a principled framework for learning posterior score functions of \emph{conditional diffusion models} by explicitly incorporating the physical measurement operator into a modular network architecture. Diff-Unfolding formulates posterior score learning as the training of an unrolled optimization scheme, where the measurement model is decoupled from the learned image prior. This design allows our method to generalize across inverse problems at inference time by simply replacing the forward operator without retraining. We theoretically justify our unrolling approach by showing that the posterior score can be derived from a composite model-based optimization formulation. Extensive experiments on image restoration and accelerated MRI show that Diff-Unfolding achieves state-of-the-art performance, improving PSNR by up to 2 dB and reducing LPIPS by $22.7\%$, while being both compact (47M parameters) and efficient (0.72 seconds per $256 \times 256$ image). An optimized C++/LibTorch implementation further reduces inference time to 0.63 seconds, underscoring the practicality of our approach.

UGoDIT: Unsupervised Group Deep Image Prior Via Transferable Weights

Shijun Liang, Ismail R. Alkhouri, Siddhant Gautam, Qing Qu, Saiprasad Ravishankar

arxiv logopreprintMay 16 2025
Recent advances in data-centric deep generative models have led to significant progress in solving inverse imaging problems. However, these models (e.g., diffusion models (DMs)) typically require large amounts of fully sampled (clean) training data, which is often impractical in medical and scientific settings such as dynamic imaging. On the other hand, training-data-free approaches like the Deep Image Prior (DIP) do not require clean ground-truth images but suffer from noise overfitting and can be computationally expensive as the network parameters need to be optimized for each measurement set independently. Moreover, DIP-based methods often overlook the potential of learning a prior using a small number of sub-sampled measurements (or degraded images) available during training. In this paper, we propose UGoDIT, an Unsupervised Group DIP via Transferable weights, designed for the low-data regime where only a very small number, M, of sub-sampled measurement vectors are available during training. Our method learns a set of transferable weights by optimizing a shared encoder and M disentangled decoders. At test time, we reconstruct the unseen degraded image using a DIP network, where part of the parameters are fixed to the learned weights, while the remaining are optimized to enforce measurement consistency. We evaluate UGoDIT on both medical (multi-coil MRI) and natural (super resolution and non-linear deblurring) image recovery tasks under various settings. Compared to recent standalone DIP methods, UGoDIT provides accelerated convergence and notable improvement in reconstruction quality. Furthermore, our method achieves performance competitive with SOTA DM-based and supervised approaches, despite not requiring large amounts of clean training data.

The imaging crisis in axial spondyloarthritis.

Diekhoff T, Poddubnyy D

pubmed logopapersMay 16 2025
Imaging holds a pivotal yet contentious role in the early diagnosis of axial spondyloarthritis. Although MRI has enhanced our ability to detect early inflammatory changes, particularly bone marrow oedema in the sacroiliac joints, the poor specificity of this finding introduces a substantial risk of overdiagnosis. The well intentioned push by rheumatologists towards earlier intervention could inadvertently lead to the misclassification of mechanical or degenerative conditions (eg, osteitis condensans ilii) as inflammatory disease, especially in the absence of structural lesions. Diagnostic uncertainty is further fuelled by anatomical variability, sex differences, and suboptimal imaging protocols. Current strategies-such as quantifying bone marrow oedema and analysing its distribution patterns, and integrating clinical and laboratory data-offer partial guidance for avoiding overdiagnosis but fall short of resolving the core diagnostic dilemma. Emerging imaging technologies, including high-resolution sequences, quantitative MRI, radiomics, and artificial intelligence, could improve diagnostic precision, but these tools remain exploratory. This Viewpoint underscores the need for a shift in imaging approaches, recognising that although timely diagnosis and treatment is essential to prevent long-term structural damage, robust and reliable imaging criteria are also needed. Without such advances, the imaging field risks repeating past missteps seen in other rheumatological conditions.

Lightweight hybrid transformers-based dyslexia detection using cross-modality data.

Sait ARW, Alkhurayyif Y

pubmed logopapersMay 16 2025
Early and precise diagnosis of dyslexia is crucial for implementing timely intervention to reduce its effects. Timely identification can improve the individual's academic and cognitive performance. Traditional dyslexia detection (DD) relies on lengthy, subjective, restricted behavioral evaluations and interviews. Due to the limitations, deep learning (DL) models have been explored to improve DD by analyzing complex neurological, behavioral, and visual data. DL architectures, including convolutional neural networks (CNNs) and vision transformers (ViTs), encounter challenges in extracting meaningful patterns from cross-modality data. The lack of model interpretability and limited computational power restricts these models' generalizability across diverse datasets. To overcome these limitations, we propose an innovative model for DD using magnetic resonance imaging (MRI), electroencephalography (EEG), and handwriting images. We introduce a model, leveraging hybrid transformer-based feature extraction, including SWIN-Linformer for MRI, LeViT-Performer for handwriting images, and graph transformer networks (GTNs) with multi-attention mechanisms for EEG data. A multi-modal attention-based feature fusion network was used to fuse the extracted features in order to guarantee the integration of key multi-modal features. We enhance Dartbooster XGBoost (DXB)-based classification using Bayesian optimization with Hyperband (BOHB) algorithm. In order to reduce computational overhead, we employ a quantization-aware training technique. The local interpretable model-agnostic explanations (LIME) technique and gradient-weighted class activation mapping (Grad-CAM) were adopted to enable model interpretability. Five public repositories were used to train and test the proposed model. The experimental outcomes demonstrated that the proposed model achieves an accuracy of 99.8% with limited computational overhead, outperforming baseline models. It sets a novel standard for DD, offering potential for early identification and timely intervention. In the future, advanced feature fusion and quantization techniques can be utilized to achieve optimal results in resource-constrained environments.

FlowMRI-Net: A Generalizable Self-Supervised 4D Flow MRI Reconstruction Network.

Jacobs L, Piccirelli M, Vishnevskiy V, Kozerke S

pubmed logopapersMay 16 2025
Image reconstruction from highly undersampled 4D flow MRI data can be very time consuming and may result in significant underestimation of velocities depending on regularization, thereby limiting the applicability of the method. The objective of the present work was to develop a generalizable self-supervised deep learning-based framework for fast and accurate reconstruction of highly undersampled 4D flow MRI and to demonstrate the utility of the framework for aortic and cerebrovascular applications. The proposed deep-learning-based framework, called FlowMRI-Net, employs physics-driven unrolled optimization using a complex-valued convolutional recurrent neural network and is trained in a self-supervised manner. The generalizability of the framework is evaluated using aortic and cerebrovascular 4D flow MRI acquisitions acquired on systems from two different vendors for various undersampling factors (R=8,16,24) and compared to compressed sensing (CS-LLR) reconstructions. Evaluation includes an ablation study and a qualitative and quantitative analysis of image and velocity magnitudes. FlowMRI-Net outperforms CS-LLR for aortic 4D flow MRI reconstruction, resulting in significantly lower vectorial normalized root mean square error and mean directional errors for velocities in the thoracic aorta. Furthermore, the feasibility of FlowMRI-Net's generalizability is demonstrated for cerebrovascular 4D flow MRI reconstruction. Reconstruction times ranged from 3 to 7minutes on commodity CPU/GPU hardware. FlowMRI-Net enables fast and accurate reconstruction of highly undersampled aortic and cerebrovascular 4D flow MRI, with possible applications to other vascular territories.

A CVAE-based generative model for generalized B<sub>1</sub> inhomogeneity corrected chemical exchange saturation transfer MRI at 5 T.

Zhang R, Zhang Q, Wu Y

pubmed logopapersMay 15 2025
Chemical exchange saturation transfer (CEST) magnetic resonance imaging (MRI) has emerged as a powerful tool to image endogenous or exogenous macromolecules. CEST contrast highly depends on radiofrequency irradiation B<sub>1</sub> level. Spatial inhomogeneity of B<sub>1</sub> field would bias CEST measurement. Conventional interpolation-based B<sub>1</sub> correction method required CEST dataset acquisition under multiple B<sub>1</sub> levels, substantially prolonging scan time. The recently proposed supervised deep learning approach reconstructed B<sub>1</sub> inhomogeneity corrected CEST effect at the identical B<sub>1</sub> as of the training data, hindering its generalization to other B<sub>1</sub> levels. In this study, we proposed a Conditional Variational Autoencoder (CVAE)-based generative model to generate B<sub>1</sub> inhomogeneity corrected Z spectra from single CEST acquisition. The model was trained from pixel-wise source-target paired Z spectra under multiple B<sub>1</sub> with target B<sub>1</sub> as a conditional variable. Numerical simulation and healthy human brain imaging at 5 T were respectively performed to evaluate the performance of proposed model in B<sub>1</sub> inhomogeneity corrected CEST MRI. Results showed that the generated B<sub>1</sub>-corrected Z spectra agreed well with the reference averaged from regions with subtle B<sub>1</sub> inhomogeneity. Moreover, the performance of the proposed model in correcting B<sub>1</sub> inhomogeneity in APT CEST effect, as measured by both MTR<sub>asym</sub> and [Formula: see text] at 3.5 ppm, were superior over conventional Z/contrast-B<sub>1</sub>-interpolation and other deep learning methods, especially when target B<sub>1</sub> were not included in sampling or training dataset. In summary, the proposed model allows generalized B<sub>1</sub> inhomogeneity correction, benefiting quantitative CEST MRI in clinical routines.

MIMI-ONET: Multi-Modal image augmentation via Butterfly Optimized neural network for Huntington DiseaseDetection.

Amudaria S, Jawhar SJ

pubmed logopapersMay 15 2025
Huntington's disease (HD) is a chronic neurodegenerative ailment that affects cognitive decline, motor impairment, and psychiatric symptoms. However, the existing HD detection methods are struggle with limited annotated datasets that restricts their generalization performance. This research work proposes a novel MIMI-ONET for primary detection of HD using augmented multi-modal brain MRI images. The two-dimensional stationary wavelet transform (2DSWT) decomposes the MRI images into different frequency wavelet sub-bands. These sub-bands are enhanced with Contract Stretching Adaptive Histogram Equalization (CSAHE) and Multi-scale Adaptive Retinex (MSAR) by reducing the irrelevant distortions. The proposed MIMI-ONET introduces a Hepta Generative Adversarial Network (Hepta-GAN) to generates different noise-free HD images based on hepta azimuth angles (45°, 90°, 135°, 180°, 225°, 270°, 315°). Hepta-GAN incorporates Affine Estimation Module (AEM) to extract the multi-scale features using dilated convolutional layers for efficient HD image generation. Moreover, Hepta-GAN is normalized with Butterfly Optimization (BO) algorithm for enhancing augmentation performance by balancing the parameters. Finally, the generated images are given to Deep neural network (DNN) for the classification of normal control (NC), Adult-Onset HD (AHD) and Juvenile HD (JHD) cases. The ability of the proposed MIMI-ONET is evaluated with precision, specificity, f1 score, recall, and accuracy, PSNR and MSE. From the experimental results, the proposed MIMI-ONET attains the accuracy of 98.85% and reaches PSNR value of 48.05 based on the gathered Image-HD dataset. The proposed MIMI-ONET increases the overall accuracy of 9.96%, 1.85%, 5.91%, 13.80% and 13.5% for 3DCNN, KNN, FCN, RNN and ML framework respectively.

Data-Agnostic Augmentations for Unknown Variations: Out-of-Distribution Generalisation in MRI Segmentation

Puru Vaish, Felix Meister, Tobias Heimann, Christoph Brune, Jelmer M. Wolterink

arxiv logopreprintMay 15 2025
Medical image segmentation models are often trained on curated datasets, leading to performance degradation when deployed in real-world clinical settings due to mismatches between training and test distributions. While data augmentation techniques are widely used to address these challenges, traditional visually consistent augmentation strategies lack the robustness needed for diverse real-world scenarios. In this work, we systematically evaluate alternative augmentation strategies, focusing on MixUp and Auxiliary Fourier Augmentation. These methods mitigate the effects of multiple variations without explicitly targeting specific sources of distribution shifts. We demonstrate how these techniques significantly improve out-of-distribution generalization and robustness to imaging variations across a wide range of transformations in cardiac cine MRI and prostate MRI segmentation. We quantitatively find that these augmentation methods enhance learned feature representations by promoting separability and compactness. Additionally, we highlight how their integration into nnU-Net training pipelines provides an easy-to-implement, effective solution for enhancing the reliability of medical segmentation models in real-world applications.
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