Tractometry uses diffusion-weighted magnetic resonance imaging (dMRI) to assess physical properties of brain connections. Here, we present an integrative ecosystem of software that performs all steps of tractometry: post-processing of dMRI data, delineation of major white matter pathways, and modeling of the tissue properties within them. This ecosystem also provides a set of interoperable and extensible tools for visualization and interpretation of the results that extract insights from these measurements. These include novel machine learning and statistical analysis methods adapted to the characteristic structure of tract-based data. We benchmark the performance of these statistical analysis methods in different datasets and analysis tasks, including hypothesis testing on group differences and predictive analysis of subject age. We also demonstrate that computational advances implemented in the software offer orders of magnitude of acceleration. Taken together, these open-source software tools-freely available at https://tractometry.org-provide a transformative environment for the analysis of dMRI data.

With the rapid development of artificial intelligence (AI), AI-assisted medical imaging analysis demonstrates remarkable performance in early lung cancer screening. However, the costly annotation process and privacy concerns limit the construction of large-scale medical datasets, hampering the further application of AI in healthcare. To address the data scarcity in lung cancer screening, we propose Lung-DDPM, a thoracic CT image synthesis approach that effectively generates high-fidelity 3D synthetic CT images, which prove helpful in downstream lung nodule segmentation tasks. Our method is based on semantic layout-guided denoising diffusion probabilistic models (DDPM), enabling anatomically reasonable, seamless, and consistent sample generation even from incomplete semantic layouts. Our results suggest that the proposed method outperforms other state-of-the-art (SOTA) generative models in image quality evaluation and downstream lung nodule segmentation tasks. Specifically, Lung-DDPM achieved superior performance on our large validation cohort, with a Fréchet inception distance (FID) of 0.0047, maximum mean discrepancy (MMD) of 0.0070, and mean squared error (MSE) of 0.0024. These results were 7.4×, 3.1×, and 29.5× better than the second-best competitors, respectively. Furthermore, the lung nodule segmentation model, trained on a dataset combining real and Lung-DDPM-generated synthetic samples, attained a Dice Coefficient (Dice) of 0.3914 and sensitivity of 0.4393. This represents 8.8% and 18.6% improvements in Dice and sensitivity compared to the model trained solely on real samples. The experimental results highlight Lung-DDPM's potential for a broader range of medical imaging applications, such as general tumor segmentation, cancer survival estimation, and risk prediction. The code and pretrained models are available at https://github.com/Manem-Lab/Lung-DDPM/.

Deep learning models often struggle to maintain generalizability in medical imaging, particularly under domain-fracture scenarios where distribution shifts arise from varying imaging techniques, acquisition protocols, patient populations, demographics, and equipment. In practice, each hospital may need to train distinct models - differing in learning task, width, and depth - to match local data. For example, one hospital may use Euclidean architectures such as MLPs and CNNs for tabular or grid-like image data, while another may require non-Euclidean architectures such as graph neural networks (GNNs) for irregular data like brain connectomes. How to train such heterogeneous models coherently across datasets, while enhancing each model's generalizability, remains an open problem. We propose unified learning, a new paradigm that encodes each model into a graph representation, enabling unification in a shared graph learning space. A GNN then guides optimization of these unified models. By decoupling parameters of individual models and controlling them through a unified GNN (uGNN), our method supports parameter sharing and knowledge transfer across varying architectures (MLPs, CNNs, GNNs) and distributions, improving generalizability. Evaluations on MorphoMNIST and two MedMNIST benchmarks - PneumoniaMNIST and BreastMNIST - show that unified learning boosts performance when models are trained on unique distributions and tested on mixed ones, demonstrating strong robustness to unseen data with large distribution shifts. Code and benchmarks: https://github.com/basiralab/uGNN

Metal artifacts, caused by high-density metallic implants in computed tomography (CT) imaging, severely degrade image quality, complicating diagnosis and treatment planning. While existing deep learning algorithms have achieved notable success in Metal Artifact Reduction (MAR), they often struggle to suppress artifacts while preserving structural details. To address this challenge, we propose FIND-Net (Fourier-Integrated Network with Dictionary Kernels), a novel MAR framework that integrates frequency and spatial domain processing to achieve superior artifact suppression and structural preservation. FIND-Net incorporates Fast Fourier Convolution (FFC) layers and trainable Gaussian filtering, treating MAR as a hybrid task operating in both spatial and frequency domains. This approach enhances global contextual understanding and frequency selectivity, effectively reducing artifacts while maintaining anatomical structures. Experiments on synthetic datasets show that FIND-Net achieves statistically significant improvements over state-of-the-art MAR methods, with a 3.07% MAE reduction, 0.18% SSIM increase, and 0.90% PSNR improvement, confirming robustness across varying artifact complexities. Furthermore, evaluations on real-world clinical CT scans confirm FIND-Net's ability to minimize modifications to clean anatomical regions while effectively suppressing metal-induced distortions. These findings highlight FIND-Net's potential for advancing MAR performance, offering superior structural preservation and improved clinical applicability. Code is available at https://github.com/Farid-Tasharofi/FIND-Net

Sparse-view computed tomography (CT) reduces radiation exposure by subsampling projection views, but conventional reconstruction methods produce severe streak artifacts with undersampled data. While deep-learning-based methods enable single-step artifact suppression, they often produce over-smoothed results under significant sparsity. Though diffusion models improve reconstruction via iterative refinement and generative priors, they require hundreds of sampling steps and struggle with stability in highly sparse regimes. To tackle these concerns, we present the Cross-view Generalized Diffusion Model (CvG-Diff), which reformulates sparse-view CT reconstruction as a generalized diffusion process. Unlike existing diffusion approaches that rely on stochastic Gaussian degradation, CvG-Diff explicitly models image-domain artifacts caused by angular subsampling as a deterministic degradation operator, leveraging correlations across sparse-view CT at different sample rates. To address the inherent artifact propagation and inefficiency of sequential sampling in generalized diffusion model, we introduce two innovations: Error-Propagating Composite Training (EPCT), which facilitates identifying error-prone regions and suppresses propagated artifacts, and Semantic-Prioritized Dual-Phase Sampling (SPDPS), an adaptive strategy that prioritizes semantic correctness before detail refinement. Together, these innovations enable CvG-Diff to achieve high-quality reconstructions with minimal iterations, achieving 38.34 dB PSNR and 0.9518 SSIM for 18-view CT using only \textbf{10} steps on AAPM-LDCT dataset. Extensive experiments demonstrate the superiority of CvG-Diff over state-of-the-art sparse-view CT reconstruction methods. The code is available at https://github.com/xmed-lab/CvG-Diff.

Advances in image registration and machine learning have recently enabled volumetric analysis of \emph{postmortem} brain tissue from conventional photographs of coronal slabs, which are routinely collected in brain banks and neuropathology laboratories worldwide. One caveat of this methodology is the requirement of segmentation of the tissue from photographs, which currently requires costly manual intervention. In this article, we present a deep learning model to automate this process. The automatic segmentation tool relies on a U-Net architecture that was trained with a combination of \textit{(i)}1,414 manually segmented images of both fixed and fresh tissue, from specimens with varying diagnoses, photographed at two different sites; and \textit{(ii)}~2,000 synthetic images with randomized contrast and corresponding masks generated from MRI scans for improved generalizability to unseen photographic setups. Automated model predictions on a subset of photographs not seen in training were analyzed to estimate performance compared to manual labels -- including both inter- and intra-rater variability. Our model achieved a median Dice score over 0.98, mean surface distance under 0.4~mm, and 95\% Hausdorff distance under 1.60~mm, which approaches inter-/intra-rater levels. Our tool is publicly available at surfer.nmr.mgh.harvard.edu/fswiki/PhotoTools.

Background: In the field of radiology and radiotherapy, accurate delineation of tissues and organs plays a crucial role in both diagnostics and therapeutics. While the gold standard remains expert-driven manual segmentation, many automatic segmentation methods are emerging. The evaluation of these methods primarily relies on traditional metrics that only incorporate geometrical properties and fail to adapt to various applications. Aims: This study aims to develop and implement a clinically relevant segmentation metric that can be adapted for use in various medical imaging applications. Methods: Bidirectional local distance was defined, and the points of the test contour were paired with points of the reference contour. After correcting for the distance between the test and reference center of mass, Euclidean distance was calculated between the paired points, and a score was given to each test point. The overall medical similarity index was calculated as the average score across all the test points. For demonstration, we used myoma and prostate datasets; nnUNet neural networks were trained for segmentation. Results: An easy-to-use, sustainable image processing pipeline was created using Python. The code is available in a public GitHub repository along with Google Colaboratory notebooks. The algorithm can handle multislice images with multiple masks per slice. Mask splitting algorithm is also provided that can separate the concave masks. We demonstrate the adaptability with prostate segmentation evaluation. Conclusions: A novel segmentation evaluation metric was implemented, and an open-access image processing pipeline was also provided, which can be easily used for automatic measurement of clinical relevance of medical image segmentation.}

Purpose: Prenatal ultrasound is a key tool in evaluating fetal structural development and detecting abnormalities, contributing to reduced perinatal complications and improved neonatal survival. Accurate identification of standard fetal torso planes is essential for reliable assessment and personalized prenatal care. However, limitations such as low contrast and unclear texture details in ultrasound imaging pose significant challenges for fine-grained anatomical recognition. Methods: We propose a novel Multi-Contrast Fusion Module (MCFM) to enhance the model's ability to extract detailed information from ultrasound images. MCFM operates exclusively on the lower layers of the neural network, directly processing raw ultrasound data. By assigning attention weights to image representations under different contrast conditions, the module enhances feature modeling while explicitly maintaining minimal parameter overhead. Results: The proposed MCFM was evaluated on a curated dataset of fetal torso plane ultrasound images. Experimental results demonstrate that MCFM substantially improves recognition performance, with a minimal increase in model complexity. The integration of multi-contrast attention enables the model to better capture subtle anatomical structures, contributing to higher classification accuracy and clinical reliability. Conclusions: Our method provides an effective solution for improving fetal torso plane recognition in ultrasound imaging. By enhancing feature representation through multi-contrast fusion, the proposed approach supports clinicians in achieving more accurate and consistent diagnoses, demonstrating strong potential for clinical adoption in prenatal screening. The codes are available at https://github.com/sysll/MCFM.

KonfAI is a modular, extensible, and fully configurable deep learning framework specifically designed for medical imaging tasks. It enables users to define complete training, inference, and evaluation workflows through structured YAML configuration files, without modifying the underlying code. This declarative approach enhances reproducibility, transparency, and experimental traceability while reducing development time. Beyond the capabilities of standard pipelines, KonfAI provides native abstractions for advanced strategies including patch-based learning, test-time augmentation, model ensembling, and direct access to intermediate feature representations for deep supervision. It also supports complex multi-model training setups such as generative adversarial architectures. Thanks to its modular and extensible architecture, KonfAI can easily accommodate custom models, loss functions, and data processing components. The framework has been successfully applied to segmentation, registration, and image synthesis tasks, and has contributed to top-ranking results in several international medical imaging challenges. KonfAI is open source and available at \href{https://github.com/vboussot/KonfAI}{https://github.com/vboussot/KonfAI}.

The rapid growth of multimodal medical imaging data presents significant storage and transmission challenges, particularly in resource-constrained clinical settings. We propose NEURAL, a novel framework that addresses this by using semantics-guided data compression. Our approach repurposes cross-attention scores between the image and its radiological report from a fine-tuned generative vision-language model to structurally prune chest X-rays, preserving only diagnostically critical regions. This process transforms the image into a highly compressed, graph representation. This unified graph-based representation fuses the pruned visual graph with a knowledge graph derived from the clinical report, creating a universal data structure that simplifies downstream modeling. Validated on the MIMIC-CXR and CheXpert Plus dataset for pneumonia detection, NEURAL achieves a 93.4-97.7\% reduction in image data size while maintaining a high diagnostic performance of 0.88-0.95 AUC, outperforming other baseline models that use uncompressed data. By creating a persistent, task-agnostic data asset, NEURAL resolves the trade-off between data size and clinical utility, enabling efficient workflows and teleradiology without sacrificing performance. Our NEURAL code is available at https://github.com/basiralab/NEURAL.