Accurate multi-modal medical image translation requires ha-rmonizing global anatomical semantics and local structural fidelity, a challenge complicated by intermodality information loss and structural distortion. We propose ABS-Mamba, a novel architecture integrating the Segment Anything Model 2 (SAM2) for organ-aware semantic representation, specialized convolutional neural networks (CNNs) for preserving modality-specific edge and texture details, and Mamba's selective state-space modeling for efficient long- and short-range feature dependencies. Structurally, our dual-resolution framework leverages SAM2's image encoder to capture organ-scale semantics from high-resolution inputs, while a parallel CNNs branch extracts fine-grained local features. The Robust Feature Fusion Network (RFFN) integrates these epresentations, and the Bidirectional Mamba Residual Network (BMRN) models spatial dependencies using spiral scanning and bidirectional state-space dynamics. A three-stage skip fusion decoder enhances edge and texture fidelity. We employ Efficient Low-Rank Adaptation (LoRA+) fine-tuning to enable precise domain specialization while maintaining the foundational capabilities of the pre-trained components. Extensive experimental validation on the SynthRAD2023 and BraTS2019 datasets demonstrates that ABS-Mamba outperforms state-of-the-art methods, delivering high-fidelity cross-modal synthesis that preserves anatomical semantics and structural details to enhance diagnostic accuracy in clinical applications. The code is available at https://github.com/gatina-yone/ABS-Mamba

AO_SCPLOWBSTRACTC_SCPLOWThe quantification of the Ki-67 labeling index (LI) is critical for assessing tumor proliferation and prognosis in tumors, yet manual scoring remains a common practice. This study presents an automated workflow for Ki-67 scoring in whole slide images (WSIs) using an Apache Groovy code script for QuPath, complemented by a Python-based post-processing script, providing cell density maps and summary tables. The tissue and cell segmentation are performed using StarDist, a deep learning model, and adaptive thresholding to classify Ki-67 positive and negative nuclei. The pipeline was applied to a cohort of 632 pediatric brain tumor cases with 734 Ki-67-stained WSIs from the Childrens Brain Tumor Network. Medulloblastoma showed the highest Ki-67 LI (median: 19.84), followed by atypical teratoid rhabdoid tumor (median: 19.36). Moderate values were observed in brainstem glioma-diffuse intrinsic pontine glioma (median: 11.50), high-grade glioma (grades 3 & 4) (median: 9.50), and ependymoma (median: 5.88). Lower indices were found in meningioma (median: 1.84), while the lowest were seen in low-grade glioma (grades 1 & 2) (median: 0.85), dysembryoplastic neuroepithelial tumor (median: 0.63), and ganglioglioma (median: 0.50). The results aligned with the consensus of the oncology, demonstrating a significant correlation in Ki-67 LI across most of the tumor families/types, with high malignancy tumors showing the highest proliferation indices and lower malignancy tumors exhibiting lower Ki-67 LI. The automated approach facilitates the assessment of large amounts of Ki-67 WSIs in research settings.

To compare the axial cranial ultrasound images of normal and open neural tube defect (NTD) fetuses using a deep learning (DL) model and to assess its predictive accuracy in identifying open NTD.It was a prospective case-control study. Axial trans-thalamic fetal ultrasound images of participants with open fetal NTD and normal controls between 14 and 28 weeks of gestation were taken after consent. The images were divided into training, testing, and validation datasets randomly in the ratio of 70:15:15. The images were further processed and classified using DL convolutional neural network (CNN) transfer learning (TL) models. The TL models were trained for 50 epochs. The data was analyzed in terms of Cohen kappa score, accuracy score, area under receiver operating curve (AUROC) score, F1 score validity, sensitivity, and specificity of the test.A total of 59 cases and 116 controls were fully followed. Efficient net B0, Visual Geometry Group (VGG), and Inception V3 TL models were used. Both Efficient net B0 and VGG16 models gave similar high training and validation accuracy (100 and 95.83%, respectively). Using inception V3, the training and validation accuracy was 98.28 and 95.83%, respectively. The sensitivity and specificity of Efficient NetB0 was 100 and 89%, respectively, and was the best.The analysis of the changes in axial images of the fetal cranium using the DL model, Efficient Net B0 proved to be an effective model to be used in clinical application for the identification of open NTD. · Open spina bifida is often missed due to the nonrecognition of the lemon sign on ultrasound.. · Image classification using DL identified open spina bifida with excellent accuracy.. · The research is clinically relevant in low- and middle-income countries..

Alzheimer's disease (AD), a progressive neurodegenerative disorder, is the leading cause of dementia worldwide and remains incurable once it begins. Therefore, early and accurate diagnosis is essential for effective intervention. Leveraging recent advances in deep learning, this study proposes a novel diagnostic model based on the 3D-ResNet architecture to classify three cognitive states: AD, mild cognitive impairment (MCI), and cognitively normal (CN) individuals, using MRI data. The model integrates the strengths of ResNet and 3D convolutional neural networks (3D-CNN), and incorporates a special attention mechanism(SAM) within the residual structure to enhance feature representation. The study utilized the ADNI dataset, comprising 800 brain MRI scans. The dataset was split in a 7:3 ratio for training and testing, and the network was trained using data augmentation and cross-validation strategies. The proposed model achieved 92.33% accuracy in the three-class classification task, and 97.61%, 95.83%, and 93.42% accuracy in binary classifications of AD vs. CN, AD vs. MCI, and CN vs. MCI, respectively, outperforming existing state-of-the-art methods. Furthermore, Grad-CAM heatmaps and 3D MRI reconstructions revealed that the cerebral cortex and hippocampus are critical regions for AD classification. These findings demonstrate a robust and interpretable AI-based diagnostic framework for AD, providing valuable technical support for its timely detection and clinical intervention.

Accurate cortical surface parcellation is essential for elucidating brain organizational principles, functional mechanisms, and the neural substrates underlying higher cognitive and emotional processes. However, the cortical surface is a highly folded complex geometry, and large regional variations make the analysis of surface data challenging. Current methods rely on geometric simplification, such as spherical expansion, which takes hours for spherical mapping and registration, a popular but costly process that does not take full advantage of inherent structural information. In this study, we propose an Attention-guided Deep Graph Convolutional network (ADGCN) for end-to-end parcellation on primitive cortical surface manifolds. ADGCN consists of a deep graph convolutional layer with a symmetrical U-shaped structure, which enables it to effectively transmit detailed information of the original brain map and learn the complex graph structure, help the network enhance feature extraction capability. What's more, we introduce the Squeeze and Excitation (SE) module, which enables the network to better capture key features, suppress unimportant features, and significantly improve parcellation performance with a small amount of computation. We evaluated the model on a public dataset of 100 artificially labeled brain surfaces. Compared with other methods, the proposed network achieves Dice coefficient of 88.53% and an accuracy of 90.27%. The network can segment the cortex directly in the original domain, and has the advantages of high efficiency, simple operation and strong interpretability. This approach facilitates the investigation of cortical changes during development, aging, and disease progression, with the potential to enhance the accuracy of neurological disease diagnosis and the objectivity of treatment efficacy evaluation.

Accurate quantitative PET imaging in neurological studies requires proper attenuation correction. MRI-guided attenuation correction in PET/MRI remains challenging owing to the lack of direct relationship between MRI intensities and linear attenuation coefficients. This study aims at generating accurate patient-specific synthetic CT volumes, attenuation maps, and attenuation correction factor (ACF) sinograms with continuous values utilizing a combination of machine learning algorithms, image processing techniques, and voxel-based radiomics feature extraction approaches. Brain MR images of ten healthy volunteers were acquired using IR-pointwise encoding time reduction with radial acquisition (IR-PETRA) and VIBE-Dixon techniques. synthetic CT (SCT) images, attenuation maps, and attenuation correction factors (ACFs) were generated using the LightGBM, a fast and accurate machine learning algorithm, from the radiomics-based and image processing-based feature maps of MR images. Additionally, ultra-low-dose CT images of the same volunteers were acquired and served as the standard of reference for evaluation. The SCT images, attenuation maps, and ACF sinograms were assessed using qualitative and quantitative evaluation metrics and compared against their corresponding reference images, attenuation maps, and ACF sinograms. The voxel-wise and volume-wise comparison between synthetic and reference CT images yielded an average mean absolute error of 60.75 ± 8.8 HUs, an average structural similarity index of 0.88 ± 0.02, and an average peak signal-to-noise ratio of 32.83 ± 2.74 dB. Additionally, we compared MRI-based attenuation maps and ACF sinograms with their CT-based counterparts, revealing average normalized mean absolute errors of 1.48% and 1.33%, respectively. Quantitative assessments indicated higher correlations and similarities between LightGBM-synthesized CT and Reference CT images. Moreover, the cross-validation results showed the possibility of producing accurate SCT images, MRI-based attenuation maps, and ACF sinograms. This might spur the implementation of MRI-based attenuation correction on PET/MRI and dedicated brain PET scanners with lower computational time using CPU-based processors.

Identifying brain hemorrhages from magnetic resonance imaging (MRI) is a critical task for healthcare professionals. The diverse nature of MRI acquisitions with varying contrasts and orientation introduce complexity in identifying hemorrhage using neural networks. For acquisitions with varying orientations, traditional methods often involve resampling images to a fixed plane, which can lead to information loss. To address this, we propose a 3D multi-plane vision transformer (MP-ViT) for hemorrhage classification with varying orientation data. It employs two separate transformer encoders for axial and sagittal contrasts, using cross-attention to integrate information across orientations. MP-ViT also includes a modality indication vector to provide missing contrast information to the model. The effectiveness of the proposed model is demonstrated with extensive experiments on real world clinical dataset consists of 10,084 training, 1,289 validation and 1,496 test subjects. MP-ViT achieved substantial improvement in area under the curve (AUC), outperforming the vision transformer (ViT) by 5.5% and CNN-based architectures by 1.8%. These results highlight the potential of MP-ViT in improving performance for hemorrhage detection when different orientation contrasts are needed.

Neuroimaging in ALS has contributed considerable academic insights in recent years demonstrating genotype-specific topological changes decades before phenoconversion and characterising longitudinal propagation patterns in specific phenotypes. It has elucidated the radiological underpinnings of specific clinical phenomena such as pseudobulbar affect, apathy, behavioural change, spasticity, and language deficits. Academic concepts such as sexual dimorphism, motor reserve, cognitive reserve, adaptive changes, connectivity-based propagation, pathological stages, and compensatory mechanisms have also been evaluated by imaging. The underpinnings of extra-motor manifestations such as cerebellar, sensory, extrapyramidal and cognitive symptoms have been studied by purpose-designed imaging protocols. Clustering approaches have been implemented to uncover radiologically distinct disease subtypes and machine-learning models have been piloted to accurately classify individual patients into relevant diagnostic, phenotypic, and prognostic categories. Prediction models have been developed for survival in symptomatic patients and phenoconversion in asymptomatic mutation carriers. A range of novel imaging modalities have been implemented and 7 Tesla MRI platforms are increasingly being used in ALS studies. Non-ALS MND conditions, such as PLS, SBMA, and SMA, are now also being increasingly studied by quantitative neuroimaging approaches. A unifying theme of recent imaging papers is the departure from describing focal brain changes to focusing on dynamic structural and functional connectivity alterations. Progressive cortico-cortical, cortico-basal, cortico-cerebellar, cortico-bulbar, and cortico-spinal disconnection has been consistently demonstrated by recent studies and recognised as the primary driver of clinical decline. These studies have led the reconceptualisation of ALS as a "network" or "circuitry disease".

Predicting long-term functional outcomes for individuals with stroke is a significant challenge. Solving this challenge will open new opportunities for improving stroke management by informing acute interventions and guiding personalized rehabilitation strategies. The location of the stroke is a key predictor of outcomes, yet no clinically deployed tools incorporate lesion location information for outcome prognostication. This study responds to this critical need by introducing a fully automated, three-stage neuroimaging processing and machine learning pipeline that predicts personalized outcomes from clinical imaging in adult ischemic stroke patients. In the first stage, our system automatically processes raw DICOM inputs, registers the brain to a standard template, and uses deep learning models to segment the stroke lesion. In the second stage, lesion location and automatically derived network features are input into statistical models trained to predict long-term impairments from a large independent cohort of lesion patients. In the third stage, a structured PDF report is generated using a large language model that describes the strokes location, the arterial distribution, and personalized prognostic information. We demonstrate the viability of this approach in a proof-of-concept application predicting select cognitive outcomes in a stroke cohort. Brain-behavior models were pre-trained to predict chronic impairment on 28 different cognitive outcomes in a large cohort of patients with focal brain lesions (N=604). The automated pipeline used these models to predict outcomes from clinically acquired MRIs in an independent ischemic stroke cohort (N=153). Starting from raw clinical DICOM images, we show that our pipeline can generate outcome predictions for individual patients in less than 3 minutes with 96% concordance relative to methods requiring manual processing. We also show that prediction accuracy is enhanced using models that incorporate lesion location, lesion-associated network information, and demographics. Our results provide a strong proof-of-concept and lay the groundwork for developing imaging-based clinical tools for stroke outcome prognostication.

Alzheimer's disease (AD) progressively alters brain structure and function, yet the associated changes in large-scale brain network dynamics remain poorly understood. We applied the intrinsic ignition framework to resting-state functional MRI (rs-fMRI) data from AD patients, individuals with mild cognitive impairment (MCI), and cognitively healthy controls (HC) to elucidate how AD shapes intrinsic brain activity. We assessed node-metastability at the whole-brain level and in 7 canonical resting-state networks (RSNs). Our results revealed a progressive decline in dynamical complexity across the disease continuum. HC exhibited the highest node-metastability, whereas it was substantially reduced in MCI and AD patients. The cortical hierarchy of information processing was also disrupted, indicating that rich-club hubs may be selectively affected in AD progression. Furthermore, we used linear mixed-effects models to evaluate the influence of Amyloid-{beta} (A{beta}) and tau pathology on brain dynamics at both regional and whole-brain levels. We found significant associations between both protein burdens and alterations in node metastability. Lastly, a machine learning classifier trained on brain dynamics, A{beta}, and tau burden features achieved high accuracy in discriminating between disease stages. Together, our findings highlight the progressive disruption of intrinsic ignition across whole-brain and RSNs in AD and support the use of node-metastability in conjunction with proteinopathy as a novel framework for tracking disease progression.