An Adaptive, Disentangled Representation for Multidimensional MRI Reconstruction

We present a new approach for representing and reconstructing multidimensional magnetic resonance imaging (MRI) data. Our method builds on a novel, learned feature-based image representation that disentangles different types of features, such as geometry and contrast, into distinct low-dimensional latent spaces, enabling better exploitation of feature correlations in multidimensional images and incorporation of pre-learned priors specific to different feature types for reconstruction. More specifically, the disentanglement was achieved via an encoderdecoder network and image transfer training using large public data, enhanced by a style-based decoder design. A latent diffusion model was introduced to impose stronger constraints on distinct feature spaces. New reconstruction formulations and algorithms were developed to integrate the learned representation with a zero-shot selfsupervised learning adaptation and subspace modeling. The proposed method has been evaluated on accelerated T1 and T2 parameter mapping, achieving improved performance over state-of-the-art reconstruction methods, without task-specific supervised training or fine-tuning. This work offers a new strategy for learning-based multidimensional image reconstruction where only limited data are available for problem-specific or task-specific training.

MGML: A Plug-and-Play Meta-Guided Multi-Modal Learning Framework for Incomplete Multimodal Brain Tumor Segmentation

Leveraging multimodal information from Magnetic Resonance Imaging (MRI) plays a vital role in lesion segmentation, especially for brain tumors. However, in clinical practice, multimodal MRI data are often incomplete, making it challenging to fully utilize the available information. Therefore, maximizing the utilization of this incomplete multimodal information presents a crucial research challenge. We present a novel meta-guided multi-modal learning (MGML) framework that comprises two components: meta-parameterized adaptive modality fusion and consistency regularization module. The meta-parameterized adaptive modality fusion (Meta-AMF) enables the model to effectively integrate information from multiple modalities under varying input conditions. By generating adaptive soft-label supervision signals based on the available modalities, Meta-AMF explicitly promotes more coherent multimodal fusion. In addition, the consistency regularization module enhances segmentation performance and implicitly reinforces the robustness and generalization of the overall framework. Notably, our approach does not alter the original model architecture and can be conveniently integrated into the training pipeline for end-to-end model optimization. We conducted extensive experiments on the public BraTS2020 and BraTS2023 datasets. Compared to multiple state-of-the-art methods from previous years, our method achieved superior performance. On BraTS2020, for the average Dice scores across fifteen missing modality combinations, building upon the baseline, our method obtained scores of 87.55, 79.36, and 62.67 for the whole tumor (WT), the tumor core (TC), and the enhancing tumor (ET), respectively. We have made our source code publicly available at https://github.com/worldlikerr/MGML.

PathoSyn: Imaging-Pathology MRI Synthesis via Disentangled Deviation Diffusion

We present PathoSyn, a unified generative framework for Magnetic Resonance Imaging (MRI) image synthesis that reformulates imaging-pathology as a disentangled additive deviation on a stable anatomical manifold. Current generative models typically operate in the global pixel domain or rely on binary masks, these paradigms often suffer from feature entanglement, leading to corrupted anatomical substrates or structural discontinuities. PathoSyn addresses these limitations by decomposing the synthesis task into deterministic anatomical reconstruction and stochastic deviation modeling. Central to our framework is a Deviation-Space Diffusion Model designed to learn the conditional distribution of pathological residuals, thereby capturing localized intensity variations while preserving global structural integrity by construction. To ensure spatial coherence, the diffusion process is coupled with a seam-aware fusion strategy and an inference-time stabilization module, which collectively suppress boundary artifacts and produce high-fidelity internal lesion heterogeneity. PathoSyn provides a mathematically principled pipeline for generating high-fidelity patient-specific synthetic datasets, facilitating the development of robust diagnostic algorithms in low-data regimes. By allowing interpretable counterfactual disease progression modeling, the framework supports precision intervention planning and provides a controlled environment for benchmarking clinical decision-support systems. Quantitative and qualitative evaluations on tumor imaging benchmarks demonstrate that PathoSyn significantly outperforms holistic diffusion and mask-conditioned baselines in both perceptual realism and anatomical fidelity. The source code of this work will be made publicly available.

MRI-to-CT Synthesis With Cranial Suture Segmentations Using A Variational Autoencoder Framework

Quantifying normative pediatric cranial development and suture ossification is crucial for diagnosing and treating growth-related cephalic disorders. Computed tomography (CT) is widely used to evaluate cranial and sutural deformities; however, its ionizing radiation is contraindicated in children without significant abnormalities. Magnetic resonance imaging (MRI) offers radiation free scans with superior soft tissue contrast, but unlike CT, MRI cannot elucidate cranial sutures, estimate skull bone density, or assess cranial vault growth. This study proposes a deep learning driven pipeline for transforming T1 weighted MRIs of children aged 0.2 to 2 years into synthetic CTs (sCTs), predicting detailed cranial bone segmentation, generating suture probability heatmaps, and deriving direct suture segmentation from the heatmaps. With our in-house pediatric data, sCTs achieved 99% structural similarity and a Frechet inception distance of 1.01 relative to real CTs. Skull segmentation attained an average Dice coefficient of 85% across seven cranial bones, and sutures achieved 80% Dice. Equivalence of skull and suture segmentation between sCTs and real CTs was confirmed using two one sided tests (TOST p < 0.05). To our knowledge, this is the first pediatric cranial CT synthesis framework to enable suture segmentation on sCTs derived from MRI, despite MRI's limited depiction of bone and sutures. By combining robust, domain specific variational autoencoders, our method generates perceptually indistinguishable cranial sCTs from routine pediatric MRIs, bridging critical gaps in non invasive cranial evaluation.

Stochastic Siamese MAE Pretraining for Longitudinal Medical Images

Temporally aware image representations are crucial for capturing disease progression in 3D volumes of longitudinal medical datasets. However, recent state-of-the-art self-supervised learning approaches like Masked Autoencoding (MAE), despite their strong representation learning capabilities, lack temporal awareness. In this paper, we propose STAMP (Stochastic Temporal Autoencoder with Masked Pretraining), a Siamese MAE framework that encodes temporal information through a stochastic process by conditioning on the time difference between the 2 input volumes. Unlike deterministic Siamese approaches, which compare scans from different time points but fail to account for the inherent uncertainty in disease evolution, STAMP learns temporal dynamics stochastically by reframing the MAE reconstruction loss as a conditional variational inference objective. We evaluated STAMP on two OCT and one MRI datasets with multiple visits per patient. STAMP pretrained ViT models outperformed both existing temporal MAE methods and foundation models on different late stage Age-Related Macular Degeneration and Alzheimer's Disease progression prediction which require models to learn the underlying non-deterministic temporal dynamics of the diseases.

Medical Scene Reconstruction and Segmentation based on 3D Gaussian Representation

3D reconstruction of medical images is a key technology in medical image analysis and clinical diagnosis, providing structural visualization support for disease assessment and surgical planning. Traditional methods are computationally expensive and prone to structural discontinuities and loss of detail in sparse slices, making it difficult to meet clinical accuracy requirements.To address these challenges, we propose an efficient 3D reconstruction method based on 3D Gaussian and tri-plane representations. This method not only maintains the advantages of Gaussian representation in efficient rendering and geometric representation but also significantly enhances structural continuity and semantic consistency under sparse slicing conditions. Experimental results on multimodal medical datasets such as US and MRI show that our proposed method can generate high-quality, anatomically coherent, and semantically stable medical images under sparse data conditions, while significantly improving reconstruction efficiency. This provides an efficient and reliable new approach for 3D visualization and clinical analysis of medical images.

ReFRM3D: A Radiomics-enhanced Fused Residual Multiparametric 3D Network with Multi-Scale Feature Fusion for Glioma Characterization

Gliomas are among the most aggressive cancers, characterized by high mortality rates and complex diagnostic processes. Existing studies on glioma diagnosis and classification often describe issues such as high variability in imaging data, inadequate optimization of computational resources, and inefficient segmentation and classification of gliomas. To address these challenges, we propose novel techniques utilizing multi-parametric MRI data to enhance tumor segmentation and classification efficiency. Our work introduces the first-ever radiomics-enhanced fused residual multiparametric 3D network (ReFRM3D) for brain tumor characterization, which is based on a 3D U-Net architecture and features multi-scale feature fusion, hybrid upsampling, and an extended residual skip mechanism. Additionally, we propose a multi-feature tumor marker-based classifier that leverages radiomic features extracted from the segmented regions. Experimental results demonstrate significant improvements in segmentation performance across the BraTS2019, BraTS2020, and BraTS2021 datasets, achieving high Dice Similarity Coefficients (DSC) of 94.04%, 92.68%, and 93.64% for whole tumor (WT), enhancing tumor (ET), and tumor core (TC) respectively in BraTS2019; 94.09%, 92.91%, and 93.84% in BraTS2020; and 93.70%, 90.36%, and 92.13% in BraTS2021.

The Multi-View Paradigm Shift in MRI Radiomics: Predicting MGMT Methylation in Glioblastoma

Non-invasive inference of molecular tumor characteristics from medical imaging is a central goal of radiogenomics, particularly in glioblastoma (GBM), where O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation carries important prognostic and therapeutic significance. Although radiomics-based machine learning methods have shown promise for this task, conventional unimodal and early-fusion approaches are often limited by high feature redundancy and an incomplete modeling of modality-specific information. In this work, we introduce a multi-view latent representation learning framework based on variational autoencoders (VAE) to integrate complementary radiomic features derived from post-contrast T1-weighted (T1Gd) and Fluid-Attenuated Inversion Recovery (FLAIR) magnetic resonance imaging (MRI). By encoding each modality through an independent probabilistic encoder and performing fusion in a compact latent space, the proposed approach preserves modality-specific structure while enabling effective multimodal integration. The resulting latent embeddings are subsequently used for MGMT promoter methylation classification.

Unsupervised Anomaly Detection in Brain MRI via Disentangled Anatomy Learning

Detection of various lesions in brain MRI is clinically critical, but challenging due to the diversity of lesions and variability in imaging conditions. Current unsupervised learning methods detect anomalies mainly through reconstructing abnormal images into pseudo-healthy images (PHIs) by normal samples learning and then analyzing differences between images. However, these unsupervised models face two significant limitations: restricted generalizability to multi-modality and multi-center MRIs due to their reliance on the specific imaging information in normal training data, and constrained performance due to abnormal residuals propagated from input images to reconstructed PHIs. To address these limitations, two novel modules are proposed, forming a new PHI reconstruction framework. Firstly, the disentangled representation module is proposed to improve generalizability by decoupling brain MRI into imaging information and essential imaging-invariant anatomical images, ensuring that the reconstruction focuses on the anatomy. Specifically, brain anatomical priors and a differentiable one-hot encoding operator are introduced to constrain the disentanglement results and enhance the disentanglement stability. Secondly, the edge-to-image restoration module is designed to reconstruct high-quality PHIs by restoring the anatomical representation from the high-frequency edge information of anatomical images, and then recoupling the disentangled imaging information. This module not only suppresses abnormal residuals in PHI by reducing abnormal pixels input through edge-only input, but also effectively reconstructs normal regions using the preserved structural details in the edges. Evaluated on nine public datasets (4,443 patients' MRIs from multiple centers), our method outperforms 17 SOTA methods, achieving absolute improvements of +18.32% in AP and +13.64% in DSC.

A-QCF-Net: An Adaptive Quaternion Cross-Fusion Network for Multimodal Liver Tumor Segmentation from Unpaired Datasets

Multimodal medical imaging provides complementary information that is crucial for accurate delineation of pathology, but the development of deep learning models is limited by the scarcity of large datasets in which different modalities are paired and spatially aligned. This paper addresses this fundamental limitation by proposing an Adaptive Quaternion Cross-Fusion Network (A-QCF-Net) that learns a single unified segmentation model from completely separate and unpaired CT and MRI cohorts. The architecture exploits the parameter efficiency and expressive power of Quaternion Neural Networks to construct a shared feature space. At its core is the Adaptive Quaternion Cross-Fusion (A-QCF) block, a data driven attention module that enables bidirectional knowledge transfer between the two streams. By learning to modulate the flow of information dynamically, the A-QCF block allows the network to exchange abstract modality specific expertise, such as the sharp anatomical boundary information available in CT and the subtle soft tissue contrast provided by MRI. This mutual exchange regularizes and enriches the feature representations of both streams. We validate the framework by jointly training a single model on the unpaired LiTS (CT) and ATLAS (MRI) datasets. The jointly trained model achieves Tumor Dice scores of 76.7% on CT and 78.3% on MRI, significantly exceeding the strong unimodal nnU-Net baseline by margins of 5.4% and 4.7% respectively. Furthermore, comprehensive explainability analysis using Grad-CAM and Grad-CAM++ confirms that the model correctly focuses on relevant pathological structures, ensuring the learned representations are clinically meaningful. This provides a robust and clinically viable paradigm for unlocking the large unpaired imaging archives that are common in healthcare.