Reconstructing natural images from functional magnetic resonance imaging (fMRI) data remains a core challenge in natural decoding due to the mismatch between the richness of visual stimuli and the noisy, low resolution nature of fMRI signals. While recent two-stage models, combining deep variational autoencoders (VAEs) with diffusion models, have advanced this task, they treat all spatial-frequency components of the input equally. This uniform treatment forces the model to extract meaning features and suppress irrelevant noise simultaneously, limiting its effectiveness. We introduce FreqSelect, a lightweight, adaptive module that selectively filters spatial-frequency bands before encoding. By dynamically emphasizing frequencies that are most predictive of brain activity and suppressing those that are uninformative, FreqSelect acts as a content-aware gate between image features and natural data. It integrates seamlessly into standard very deep VAE-diffusion pipelines and requires no additional supervision. Evaluated on the Natural Scenes dataset, FreqSelect consistently improves reconstruction quality across both low- and high-level metrics. Beyond performance gains, the learned frequency-selection patterns offer interpretable insights into how different visual frequencies are represented in the brain. Our method generalizes across subjects and scenes, and holds promise for extension to other neuroimaging modalities, offering a principled approach to enhancing both decoding accuracy and neuroscientific interpretability.

High-grade clear cell renal cell carcinoma (ccRCC) is linked to lower survival rates and more aggressive disease progression. This study aims to assess the diagnostic performance of MRI-derived radiomics as a non-invasive approach for pre-operative differentiation of high-grade from low-grade ccRCC. A systematic search was conducted across PubMed, Scopus, and Embase. Quality assessment was performed using QUADAS-2 and METRICS. Pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and area under the curve (AUC) were estimated using a bivariate model. Separate meta-analyses were conducted for radiomics models and combined models, where the latter integrated clinical and radiological features with radiomics. Subgroup analysis was performed to identify potential sources of heterogeneity. Sensitivity analysis was conducted to identify potential outliers. A total of 15 studies comprising 2,265 patients were included, with seven and six studies contributing to the meta-analysis of radiomics and combined models, respectively. The pooled estimates of the radiomics model were as follows: sensitivity, 0.78; specificity, 0.84; PLR, 4.17; NLR, 0.28; DOR, 17.34; and AUC, 0.84. For the combined model, the pooled sensitivity, specificity, PLR, NLR, DOR, and AUC were 0.87, 0.81, 3.78, 0.21, 28.57, and 0.90, respectively. Radiomics models trained on smaller cohorts exhibited a significantly higher pooled specificity and PLR than those trained on larger cohorts. Also, radiomics models based on single-user segmentation demonstrated a significantly higher pooled specificity compared to multi-user segmentation. Radiomics has demonstrated potential as a non-invasive tool for grading ccRCC, with combined models achieving superior performance.

Alzheimer's disease (AD) is a progressive neurodegenerative disorder that severely affects memory, behavior, and cognitive function. Early and accurate diagnosis is crucial for effective intervention, yet detecting subtle changes in the early stages remains a challenge. In this study, we propose a hybrid deep learning-based multi-class classification system for AD using magnetic resonance imaging (MRI). The proposed approach integrates an improved DeepLabV3+ (IDeepLabV3+) model for lesion segmentation, followed by feature extraction using the LeNet-5 model. A novel feature selection method based on average correlation and error probability is employed to enhance classification efficiency. Finally, an Enhanced ResNext (EResNext) model is used to classify AD into four stages: non-dementia (ND), very mild dementia (VMD), mild dementia (MD), and moderate dementia (MOD). The proposed model achieves an accuracy of 98.12%, demonstrating its superior performance over existing methods. The area under the ROC curve (AUC) further validates its effectiveness, with the highest score of 0.97 for moderate dementia. This study highlights the potential of hybrid deep learning models in improving early AD detection and staging, contributing to more accurate clinical diagnosis and better patient care.

Accurate differentiation of pseudoprogression (PsP) from True Progression (TP) following radiotherapy (RT) in glioblastoma patients is crucial for optimal treatment planning. However, this task remains challenging due to the overlapping imaging characteristics of PsP and TP. This study therefore proposes a multimodal deep-learning approach utilizing complementary information from routine anatomical MR images, clinical parameters, and RT treatment planning information for improved predictive accuracy. The approach utilizes a self-supervised Vision Transformer (ViT) to encode multi-sequence MR brain volumes to effectively capture both global and local context from the high dimensional input. The encoder is trained in a self-supervised upstream task on unlabeled glioma MRI datasets from the open BraTS2021, UPenn-GBM, and UCSF-PDGM datasets (n = 2317 MRI studies) to generate compact, clinically relevant representations from FLAIR and T1 post-contrast sequences. These encoded MR inputs are then integrated with clinical data and RT treatment planning information through guided cross-modal attention, improving progression classification accuracy. This work was developed using two datasets from different centers: the Burdenko Glioblastoma Progression Dataset (n = 59) for training and validation, and the GlioCMV progression dataset from the University Hospital Erlangen (UKER) (n = 20) for testing. The proposed method achieved competitive performance, with an AUC of 75.3%, outperforming the current state-of-the-art data-driven approaches. Importantly, the proposed approach relies solely on readily available anatomical MRI sequences, clinical data, and RT treatment planning information, enhancing its clinical feasibility. The proposed approach addresses the challenge of limited data availability for PsP and TP differentiation and could allow for improved clinical decision-making and optimized treatment plans for glioblastoma patients.

Diffusion models are widely used in applications ranging from image generation to inverse problems. However, training diffusion models typically requires clean ground-truth images, which are unavailable in many applications. We introduce the Measurement Score-based diffusion Model (MSM), a novel framework that learns partial measurement scores using only noisy and subsampled measurements. MSM models the distribution of full measurements as an expectation over partial scores induced by randomized subsampling. To make the MSM representation computationally efficient, we also develop a stochastic sampling algorithm that generates full images by using a randomly selected subset of partial scores at each step. We additionally propose a new posterior sampling method for solving inverse problems that reconstructs images using these partial scores. We provide a theoretical analysis that bounds the Kullback-Leibler divergence between the distributions induced by full and stochastic sampling, establishing the accuracy of the proposed algorithm. We demonstrate the effectiveness of MSM on natural images and multi-coil MRI, showing that it can generate high-quality images and solve inverse problems -- all without access to clean training data. Code is available at https://github.com/wustl-cig/MSM.

White matter hyperintensity (WMH) is a primary manifestation of small vessel disease (SVD), leading to vascular cognitive impairment and other disorders. Accurate WMH quantification is vital for diagnosis and prognosis, but current automatic segmentation methods often fall short, especially across different datasets. The aims of this study are to develop and validate a robust deep learning segmentation method for WMH of vascular-origin. In this study, we developed a transformer-based method for the automatic segmentation of vascular-origin WMH using both 3D T1 and 3D T2-FLAIR images. Our initial dataset comprised 126 participants with varying WMH burdens due to SVD, each with manually segmented WMH masks used for training and testing. External validation was performed on two independent datasets: the WMH Segmentation Challenge 2017 dataset (170 subjects) and an in-house vascular risk factor dataset (70 subjects), which included scans acquired on eight different MRI systems at field strengths of 1.5T, 3T, and 5T. This approach enabled a comprehensive assessment of the method's generalizability across diverse imaging conditions. We further compared our method against LGA, LPA, BIANCA, UBO-detector and TrUE-Net in optimized settings. Our method consistently outperformed others, achieving a median Dice coefficient of 0.78±0.09 in our primary dataset, 0.72±0.15 in the external dataset 1, and 0.72±0.14 in the external dataset 2. The relative volume errors were 0.15±0.14, 0.50±0.86, and 0.47±1.02, respectively. The true positive rates were 0.81±0.13, 0.92±0.09, and 0.92±0.12, while the false positive rates were 0.20±0.09, 0.40±0.18, and 0.40±0.19. None of the external validation datasets were used for model training; instead, they comprise previously unseen MRI scans acquired from different scanners and protocols. This setup closely reflects real-world clinical scenarios and further demonstrates the robustness and generalizability of our model across diverse MRI systems and acquisition settings. As such, the proposed method provides a reliable solution for WMH segmentation in large-scale cohort studies.

Synthetic MRI (SyMRI) is a technique used to estimate tissue properties and generate multiple MR sequence contrasts from a single acquisition. However, image quality can be suboptimal. To evaluate a neural network approach using artificial intelligence-based direct contrast synthesis (AI-DCS) of the multi-contrast weighted images to improve image quality. This prospective, IRB approved study enrolled 50 pediatric patients undergoing clinical brain MRI. In addition to the standard of care (SOC) clinical protocol, 2D multi-delay multi-echo (MDME) sequence was obtained. SOC 3D T1-weighted (T1W), 2D T2-weighted (T2W) and 2D T2W fluid-attenuated inversion recovery (FLAIR) images from 35 patients were used to train a neural network generating synthetic T1W, T2W, and FLAIR images. Quantitative analysis of grey matter (GM) and white matter (WM) apparent signal to noise (aSNR) and grey-white matter (GWM) apparent contrast to noise (aCNR) ratios was performed. 8 patients were evaluated. When compared to SyMRI, T1W AI-DCS had better overall image quality, reduced noise/artifacts, and better subjective SNR in 100 % (16/16) of evaluations. When compared to SyMRI, T2W AI-DCS overall image quality and diagnostic confidence was better in 93.8 % (15/16) and 87.5 % (14/16) of evaluations, respectively. When compared to SyMRI, FLAIR AI-DCS was better in 93.8 % (15/16) of evaluations in overall image quality and in 100 % (16/16) of evaluations for noise/artifacts and subjective SNR. Quantitative analysis revealed higher WM aSNR compared with SyMRI (p < 0.05) for T1W, T2W and FLAIR. AI-DCS demonstrates better overall image quality than SyMRI on T1W, T2W and FLAIR.

Alzheimer's disease (AD) is a progressive neurological disorder characterized by cognitive decline due to brain cell death, typically manifesting later in life.Early and accurate detection is critical for effective disease management and treatment. This study proposes an ensemble learning framework that combines five deep learning architectures (VGG16, VGG19, ResNet50, InceptionV3, and EfficientNetB7) to improve the accuracy of AD diagnosis. We use a comprehensive dataset of 3,714 MRI brain scans collected from specialized clinics in Iraq, categorized into three classes: NonDemented (834 images), MildDemented (1,824 images), and VeryDemented (1,056 images). The proposed voting ensemble model achieves a diagnostic accuracy of 99.32% on our dataset. The effectiveness of the model is further validated on two external datasets: OASIS (achieving 86.6% accuracy) and ADNI (achieving 99.5% accuracy), demonstrating competitive performance compared to existing approaches. Moreover, the proposed model exhibits high precision and recall across all stages of dementia, providing a reliable and robust tool for early AD detection. This study highlights the effectiveness of ensemble learning in AD diagnosis and shows promise for clinical applications.

To evaluate diagnostic accuracy and image quality of deep learning (DL) cine sequences for LV and RV parameters compared to conventional balanced steady-state free precession (bSSFP) cine sequences in cardiovascular magnetic resonance (CMR). From January to April 2024, patients with clinically indicated CMR were prospectively included. LV and RV were segmented from short-axis bSSFP and DL cine sequences. LV and RV end-diastolic volume (EDV), end-systolic volume (EDV), stroke volume (SV), ejection fraction, and LV end-diastolic mass were calculated. The acquisition time of both sequences was registered. Results were compared with paired-samples t test or Wilcoxon signed-rank test. Agreement between DL cine and bSSFP was assessed using Bland-Altman plots. Image quality was graded by two readers based on blood-to-myocardium contrast, endocardial edge definition, and motion artifacts, using a 5-point Likert scale (1 = insufficient quality; 5 = excellent quality). Sixty-two patients were included (mean age: 47 ± 17 years, 41 men). No significant differences between DL cine and bSSFP were found for all LV and RV parameters (P ≥ .176). DL cine was significantly faster (1.35 ± .55 m vs 2.83 ± .79 m; P < .001). The agreement between DL cine and bSSFP was strong, with bias ranging from 45 to 1.75% for LV and from - 0.38 to 2.43% for RV. Among LV parameters, the highest agreement was obtained for ESV and SV, which fell within the acceptable limit of agreement (LOA) in 84% of cases. EDV obtained the highest agreement among RV parameters, falling within the acceptable LOA in 90% of cases. Overall image quality was comparable (median: 5, IQR: 4-5; P = .330), while endocardial edge definition of DL cine (median: 4, IQR: 4-5) was lower than bSSFP (median: 5, IQR: 4-5; P = .002). DL cine allows fast and accurate quantification of LV and RV parameters and comparable image quality with conventional bSSFP.

Artifacts in clinical MRI can compromise the performance of AI models. This study evaluates how different data augmentation strategies affect an AI model's segmentation performance under variable artifact severity. We used an AI model based on the nnU-Net architecture to automatically quantify lower limb alignment using axial T2-weighted MR images. Three versions of the AI model were trained with different augmentation strategies: (1) no augmentation ("baseline"), (2) standard nnU-net augmentations ("default"), and (3) "default" plus augmentations that emulate MR artifacts ("MRI-specific"). Model performance was tested on 600 MR image stacks (right and left; hip, knee, and ankle) from 20 healthy participants (mean age, 23 ± 3 years, 17 men), each imaged five times under standardized motion to induce artifacts. Two radiologists graded each stack's artifact severity as none, mild, moderate, and severe, and manually measured torsional angles. Segmentation quality was assessed using the Dice similarity coefficient (DSC), while torsional angles were compared between manual and automatic measurements using mean absolute deviation (MAD), intraclass correlation coefficient (ICC), and Pearson's correlation coefficient (r). Statistical analysis included parametric tests and a Linear Mixed-Effects Model. MRI-specific augmentation resulted in slightly (yet not significantly) better performance than the default strategy. Segmentation quality decreased with increasing artifact severity, which was partially mitigated by default and MRI-specific augmentations (e.g., severe artifacts, proximal femur: DSC_baseline = 0.58 ± 0.22; DSC_default = 0.72 ± 0.22; DSC_MRI-specific = 0.79 ± 0.14 [p < 0.001]). These augmentations also maintained precise torsional angle measurements (e.g., severe artifacts, femoral torsion: MAD_baseline = 20.6 ± 23.5°; MAD_default = 7.0 ± 13.0°; MAD_MRI-specific = 5.7 ± 9.5° [p < 0.001]; ICC_baseline = -0.10 [p = 0.63; 95% CI: -0.61 to 0.47]; ICC_default = 0.38 [p = 0.08; -0.17 to 0.76]; ICC_MRI-specific = 0.86 [p < 0.001; 0.62 to 0.95]; r_baseline = 0.58 [p < 0.001; 0.44 to 0.69]; r_default = 0.68 [p < 0.001; 0.56 to 0.77]; r_MRI-specific = 0.86 [p < 0.001; 0.81 to 0.9]). Motion artifacts negatively impact AI models, but general-purpose augmentations enhance robustness effectively. MRI-specific augmentations offer minimal additional benefit. Question Motion artifacts negatively impact the performance of diagnostic AI models for MRI, but mitigation methods remain largely unexplored. Findings Domain-specific augmentation during training can improve the robustness and performance of a model for quantifying lower limb alignment in the presence of severe artifacts. Clinical relevance Excellent robustness and accuracy are crucial for deploying diagnostic AI models in clinical practice. Including domain knowledge in model training can benefit clinical adoption.