The brain is a highly complex organ that manages many important tasks, including movement, memory and thinking. Brain-related conditions, like tumors and degenerative disorders, can be hard to diagnose and treat. Magnetic Resonance Imaging (MRI) serves as a key tool for identifying these conditions, offering high-resolution images of brain structures. Despite this, interpreting MRI scans can be complicated. This study tackles this challenge by conducting a comparative analysis of Vision Transformer (ViT) and Transfer Learning (TL) models such as VGG16, VGG19, Resnet50V2, MobilenetV2 for classifying brain diseases using MRI data from Bangladesh based dataset. ViT, known for their ability to capture global relationships in images, are particularly effective for medical imaging tasks. Transfer learning helps to mitigate data constraints by fine-tuning pre-trained models. Furthermore, Explainable AI (XAI) methods such as GradCAM, GradCAM++, LayerCAM, ScoreCAM, and Faster-ScoreCAM are employed to interpret model predictions. The results demonstrate that ViT surpasses transfer learning models, achieving a classification accuracy of 94.39%. The integration of XAI methods enhances model transparency, offering crucial insights to aid medical professionals in diagnosing brain diseases with greater precision.

Desmoid tumors are rare, locally invasive soft-tissue tumors with unpredictable clinical behavior. Imaging plays a crucial role in their diagnosis, measurement of disease burden, and assessment of treatment response. However, desmoid tumors' unique imaging features present challenges to conventional imaging metrics. The heterogeneous nature of these tumors, with a variable composition (fibrous, myxoid, or cellular), complicates accurate delineation of tumor boundaries and volumetric assessment. Furthermore, desmoid tumors can demonstrate prolonged stability or spontaneous regression, and biologic quiescence is often manifested by collagenization rather than bulk size reduction, making traditional size-based response criteria, such as Response Evaluation Criteria in Solid Tumors (RECIST), suboptimal. To overcome these limitations, advanced imaging techniques offer promising opportunities. Functional and parametric imaging methods, such as diffusion-weighted MRI, dynamic contrast-enhanced MRI, and T2 relaxometry, can provide insights into tumor cellularity and maturation. Radiomics and artificial intelligence approaches may enhance quantitative analysis by extracting and correlating complex imaging features with biological behavior. Moreover, imaging biomarkers could facilitate earlier detection of treatment efficacy or resistance, enabling tailored therapy. By integrating advanced imaging into clinical practice, it may be possible to refine the evaluation of disease burden and treatment response, ultimately improving the management and outcomes of patients with desmoid tumors.

Mesh reconstruction is a cornerstone process across various applications, including in-silico trials, digital twins, surgical planning, and navigation. Recent advancements in deep learning have notably enhanced mesh reconstruction speeds. Yet, traditional methods predominantly rely on deforming a standardised template mesh for individual subjects, which overlooks the unique anatomical variations between them, and may compromise the fidelity of the reconstructions. In this paper, we propose an adaptive-template-based mesh reconstruction network (ATMRN), which generates adaptive templates from the given images for the subsequent deformation, moving beyond the constraints of a singular, fixed template. Our approach, validated on cortical magnetic resonance (MR) images from the OASIS dataset, sets a new benchmark in voxel-to-cortex mesh reconstruction, achieving an average symmetric surface distance of 0.267mm across four cortical structures. Our proposed method is generic and can be easily transferred to other image modalities and anatomical structures.

PurposeTo develop a segmentation and quality control pipeline for short-axis cardiac magnetic resonance (CMR) cine images from the prospective, multi-center German National Cohort (NAKO). Materials and MethodsA deep learning model for semantic segmentation, based on the nnU-Net architecture, was applied to full-cycle short-axis cine images from 29,908 baseline participants. The primary objective was to determine data on structure and function for both ventricles (LV, RV), including end diastolic volumes (EDV), end systolic volumes (ESV), and LV myocardial mass. Quality control measures included a visual assessment of outliers in morphofunctional parameters, inter- and intra-ventricular phase differences, and LV time-volume curves (TVC). These were adjudicated using a five-point rating scale, ranging from five (excellent) to one (non-diagnostic), with ratings of three or lower subject to exclusion. The predictive value of outlier criteria for inclusion and exclusion was analyzed using receiver operating characteristics. ResultsThe segmentation model generated complete data for 29,609 participants (incomplete in 1.0%) and 5,082 cases (17.0 %) were visually assessed. Quality assurance yielded a sample of 26,899 participants with excellent or good quality (89.9%; exclusion of 1,875 participants due to image quality issues and 835 cases due to segmentation quality issues). TVC was the strongest single discriminator between included and excluded participants (AUC: 0.684). Of the two-category combinations, the pairing of TVC and phases provided the greatest improvement over TVC alone (AUC difference: 0.044; p<0.001). The best performance was observed when all three categories were combined (AUC: 0.748). Extending the quality-controlled sample to include acceptable quality ratings, a total of 28,413 (95.0%) participants were available. ConclusionThe implemented pipeline facilitated the automated segmentation of an extensive CMR dataset, integrating quality control measures. This methodology ensures that ensuing quantitative analyses are conducted with a diminished risk of bias.

A brain tumor is an abnormal growth in the brain that disrupts its functionality and poses a significant threat to human life by damaging neurons. Early detection and classification of brain tumors are crucial to prevent complications and maintain good health. Recent advancements in deep learning techniques have shown immense potential in image classification and segmentation for tumor identification and classification. In this study, we present a platform, BrainView, for detection, and segmentation of brain tumors from Magnetic Resonance Images (MRI) using deep learning. We utilized EfficientNetB7 pre-trained model to design our proposed DeepBrainNet classification model for analyzing brain MRI images to classify its type. We also proposed a EfficinetNetB7 based image segmentation model, called the EffB7-UNet, for tumor localization. Experimental results show significantly high classification (99.96%) and segmentation (92.734%) accuracies for our proposed models. Finally, we discuss the contours of a cloud application for BrainView using Flask and Flutter to help researchers and clinicians use our machine learning models online for research purposes.

To develop an integrative radiopathomic model based on deep learning to predict overall survival (OS) in locally advanced nasopharyngeal carcinoma (LANPC) patients. A cohort of 343 LANPC patients with pretreatment MRI and whole slide image (WSI) were randomly divided into training (n = 202), validation (n = 91), and external test (n = 50) sets. For WSIs, a self-attention mechanism was employed to assess the significance of different patches for the prognostic task, aggregating them into a WSI-level representation. For MRI, a multilayer perceptron was used to encode the extracted radiomic features, resulting in an MRI-level representation. These were combined in a multimodal fusion model to produce prognostic predictions. Model performances were evaluated using the concordance index (C-index), and Kaplan-Meier curves were employed for risk stratification. To enhance model interpretability, attention-based and Integrated Gradients techniques were applied to explain how WSIs and MRI features contribute to prognosis predictions. The radiopathomics model achieved high predictive accuracy in predicting the OS, with a C-index of 0.755 (95 % CI: 0.673-0.838) and 0.744 (95 % CI: 0.623-0.808) in the training and validation sets, respectively, outperforming single-modality models (radiomic signature: 0.636, 95 % CI: 0.584-0.688; deep pathomic signature: 0.736, 95 % CI: 0.684-0.810). In the external test, similar findings were observed for the predictive performance of the radiopathomics, radiomic signature, and deep pathomic signature, with their C-indices being 0.735, 0.626, and 0.660 respectively. The radiopathomics model effectively stratified patients into high- and low-risk groups (P < 0.001). Additionally, attention heatmaps revealed that high-attention regions corresponded with tumor areas in both risk groups. n: The radiopathomics model holds promise for predicting clinical outcomes in LANPC patients, offering a potential tool for improving clinical decision-making.

Magnetic Resonance Imaging (MRI) is highly susceptible to motion artifacts due to the extended acquisition times required for k-space sampling. These artifacts can compromise diagnostic utility, particularly for dynamic imaging. We propose a novel alternating minimization framework that leverages a bespoke diffusion model to jointly reconstruct and correct non-rigid motion-corrupted k-space data. The diffusion model uses a coarse-to-fine denoising strategy to capture large overall motion and reconstruct the lower frequencies of the image first, providing a better inductive bias for motion estimation than that of standard diffusion models. We demonstrate the performance of our approach on both real-world cine cardiac MRI datasets and complex simulated rigid and non-rigid deformations, even when each motion state is undersampled by a factor of 64x. Additionally, our method is agnostic to sampling patterns, anatomical variations, and MRI scanning protocols, as long as some low frequency components are sampled during each motion state.

The precise and timely diagnosis of brain tumors is essential for accelerating patient recovery and preserving lives. Brain tumors exhibit a variety of sizes, shapes, and visual characteristics, requiring individualized treatment strategies for each patient. Radiologists require considerable proficiency to manually detect brain malignancies. However, tumor recognition remains inefficient, imprecise, and labor-intensive in manual procedures, underscoring the need for automated methods. This study introduces an effective approach for identifying brain lesions in magnetic resonance imaging (MRI) images, minimizing dependence on manual intervention. The proposed method improves image clarity by combining guided filtering techniques with anisotropic Gaussian side windows (AGSW). A morphological analysis is conducted prior to segmentation to exclude non-tumor regions from the enhanced MRI images. Deep neural networks segment the images, extracting high-quality regions of interest (ROIs) and multiscale features. Identifying salient elements is essential and is accomplished through an attention module that isolates distinctive features while eliminating irrelevant information. An ensemble model is employed to classify brain tumors into different categories. The proposed technique achieves an overall accuracy of 99.94% and 99.67% on the publicly available brain tumor datasets BraTS2020 and Figshare, respectively. Furthermore, it surpasses existing technologies in terms of automation and robustness, thereby enhancing the entire diagnostic process.

Deep learning methods provide enormous promise in automating manually intense tasks such as medical image segmentation and provide workflow assistance to clinical experts. Deep neural networks (DNN) require a significant amount of training examples and a variety of expert opinions to capture the nuances and the context, a challenging proposition in oncological studies (H. Wang et al., Nature, vol. 620, no. 7972, pp. 47-60, Aug 2023). Inter-reader variability among clinical experts is a real-world problem that severely impacts the generalization of DNN reproducibility. This study proposes quantifying the variability in DNN performance using expert opinions and exploring strategies to train the network and adapt between expert opinions. We address the inter-reader variability problem in the context of prostate gland segmentation using a well-studied DNN, the 3D U-Net model. Reference data includes magnetic resonance imaging (MRI, T2-weighted) with prostate glandular anatomy annotations from two expert readers (R#1, n = 342 and R#2, n = 204). 3D U-Net was trained and tested with individual expert examples (R#1 and R#2) and had an average Dice coefficient of 0.825 (CI, [0.81 0.84]) and 0.85 (CI, [0.82 0.88]), respectively. Combined training with a representative cohort proportion (R#1, n = 100 and R#2, n = 150) yielded enhanced model reproducibility across readers, achieving an average test Dice coefficient of 0.863 (CI, [0.85 0.87]) for R#1 and 0.869 (CI, [0.87 0.88]) for R#2. We re-evaluated the model performance across the gland volumes (large, small) and found improved performance for large gland size with an average Dice coefficient to be at 0.846 [CI, 0.82 0.87] and 0.872 [CI, 0.86 0.89] for R#1 and R#2, respectively, estimated using fivefold cross-validation. Performance for small gland sizes diminished with average Dice of 0.8 [0.79, 0.82] and 0.8 [0.79, 0.83] for R#1 and R#2, respectively.

This study centers around the competition between Convolutional Neural Networks (CNNs) with large convolutional kernels and Vision Transformers in the domain of computer vision, delving deeply into the issues pertaining to parameters and computational complexity that stem from the utilization of large convolutional kernels. Even though the size of the convolutional kernels has been extended up to 51×51, the enhancement of performance has hit a plateau, and moreover, striped convolution incurs a performance degradation. Enlightened by the hierarchical visual processing mechanism inherent in humans, this research innovatively incorporates a shared parameter mechanism for large convolutional kernels. It synergizes the expansion of the receptive field enabled by large convolutional kernels with the extraction of fine-grained features facilitated by small convolutional kernels. To address the surging number of parameters, a meticulously designed parameter sharing mechanism is employed, featuring fine-grained processing in the central region of the convolutional kernel and wide-ranging parameter sharing in the periphery. This not only curtails the parameter count and mitigates the model complexity but also sustains the model's capacity to capture extensive spatial relationships. Additionally, in light of the problems of spatial feature information loss and augmented memory access during the 1×1 convolutional channel compression phase, this study further puts forward a dynamic channel sampling approach, which markedly elevates the accuracy of tumor subregion segmentation. To authenticate the efficacy of the proposed methodology, a comprehensive evaluation has been conducted on three brain tumor segmentation datasets, namely BraTs2020, BraTs2024, and Medical Segmentation Decathlon Brain 2018. The experimental results evince that the proposed model surpasses the current mainstream ConvNet and Transformer architectures across all performance metrics, proffering novel research perspectives and technical stratagems for the realm of medical image segmentation.