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Moving Beyond CT Body Composition Analysis: Using Style Transfer for Bringing CT-Based Fully-Automated Body Composition Analysis to T2-Weighted MRI Sequences.

Haubold J, Pollok OB, Holtkamp M, Salhöfer L, Schmidt CS, Bojahr C, Straus J, Schaarschmidt BM, Borys K, Kohnke J, Wen Y, Opitz M, Umutlu L, Forsting M, Friedrich CM, Nensa F, Hosch R

pubmed logopapersAug 1 2025
Deep learning for body composition analysis (BCA) is gaining traction in clinical research, offering rapid and automated ways to measure body features like muscle or fat volume. However, most current methods prioritize computed tomography (CT) over magnetic resonance imaging (MRI). This study presents a deep learning approach for automatic BCA using MR T2-weighted sequences. Initial BCA segmentations (10 body regions and 4 body parts) were generated by mapping CT segmentations from body and organ analysis (BOA) model to synthetic MR images created using an in-house trained CycleGAN. In total, 30 synthetic data pairs were used to train an initial nnU-Net V2 in 3D, and this preliminary model was then applied to segment 120 real T2-weighted MRI sequences from 120 patients (46% female) with a median age of 56 (interquartile range, 17.75), generating early segmentation proposals. These proposals were refined by human annotators, and nnU-Net V2 2D and 3D models were trained using 5-fold cross-validation on this optimized dataset of real MR images. Performance was evaluated using Sørensen-Dice, Surface Dice, and Hausdorff Distance metrics including 95% confidence intervals for cross-validation and ensemble models. The 3D ensemble segmentation model achieved the highest Dice scores for the body region classes: bone 0.926 (95% confidence interval [CI], 0.914-0.937), muscle 0.968 (95% CI, 0.961-0.975), subcutaneous fat 0.98 (95% CI, 0.971-0.986), nervous system 0.973 (95% CI, 0.965-0.98), thoracic cavity 0.978 (95% CI, 0.969-0.984), abdominal cavity 0.989 (95% CI, 0.986-0.991), mediastinum 0.92 (95% CI, 0.901-0.936), pericardium 0.945 (95% CI, 0.924-0.96), brain 0.966 (95% CI, 0.927-0.989), and glands 0.905 (95% CI, 0.886-0.921). Furthermore, body part 2D ensemble model reached the highest Dice scores for all labels: arms 0.952 (95% CI, 0.937-0.965), head + neck 0.965 (95% CI, 0.953-0.976), legs 0.978 (95% CI, 0.968-0.988), and torso 0.99 (95% CI, 0.988-0.991). The overall average Dice across body parts (2D = 0.971, 3D = 0.969, P = ns) and body regions (2D = 0.935, 3D = 0.955, P < 0.001) ensemble models indicates stable performance across all classes. The presented approach facilitates efficient and automated extraction of BCA parameters from T2-weighted MRI sequences, providing precise and detailed body composition information across various regions and body parts.

DICOM De-Identification via Hybrid AI and Rule-Based Framework for Scalable, Uncertainty-Aware Redaction

Kyle Naddeo, Nikolas Koutsoubis, Rahul Krish, Ghulam Rasool, Nidhal Bouaynaya, Tony OSullivan, Raj Krish

arxiv logopreprintJul 31 2025
Access to medical imaging and associated text data has the potential to drive major advances in healthcare research and patient outcomes. However, the presence of Protected Health Information (PHI) and Personally Identifiable Information (PII) in Digital Imaging and Communications in Medicine (DICOM) files presents a significant barrier to the ethical and secure sharing of imaging datasets. This paper presents a hybrid de-identification framework developed by Impact Business Information Solutions (IBIS) that combines rule-based and AI-driven techniques, and rigorous uncertainty quantification for comprehensive PHI/PII removal from both metadata and pixel data. Our approach begins with a two-tiered rule-based system targeting explicit and inferred metadata elements, further augmented by a large language model (LLM) fine-tuned for Named Entity Recognition (NER), and trained on a suite of synthetic datasets simulating realistic clinical PHI/PII. For pixel data, we employ an uncertainty-aware Faster R-CNN model to localize embedded text, extract candidate PHI via Optical Character Recognition (OCR), and apply the NER pipeline for final redaction. Crucially, uncertainty quantification provides confidence measures for AI-based detections to enhance automation reliability and enable informed human-in-the-loop verification to manage residual risks. This uncertainty-aware deidentification framework achieves robust performance across benchmark datasets and regulatory standards, including DICOM, HIPAA, and TCIA compliance metrics. By combining scalable automation, uncertainty quantification, and rigorous quality assurance, our solution addresses critical challenges in medical data de-identification and supports the secure, ethical, and trustworthy release of imaging data for research.

Medical Image De-Identification Benchmark Challenge

Linmin Pei, Granger Sutton, Michael Rutherford, Ulrike Wagner, Tracy Nolan, Kirk Smith, Phillip Farmer, Peter Gu, Ambar Rana, Kailing Chen, Thomas Ferleman, Brian Park, Ye Wu, Jordan Kojouharov, Gargi Singh, Jon Lemon, Tyler Willis, Milos Vukadinovic, Grant Duffy, Bryan He, David Ouyang, Marco Pereanez, Daniel Samber, Derek A. Smith, Christopher Cannistraci, Zahi Fayad, David S. Mendelson, Michele Bufano, Elmar Kotter, Hamideh Haghiri, Rajesh Baidya, Stefan Dvoretskii, Klaus H. Maier-Hein, Marco Nolden, Christopher Ablett, Silvia Siggillino, Sandeep Kaushik, Hongzhu Jiang, Sihan Xie, Zhiyu Wan, Alex Michie, Simon J Doran, Angeline Aurelia Waly, Felix A. Nathaniel Liang, Humam Arshad Mustagfirin, Michelle Grace Felicia, Kuo Po Chih, Rahul Krish, Ghulam Rasool, Nidhal Bouaynaya, Nikolas Koutsoubis, Kyle Naddeo, Kartik Pandit, Tony O'Sullivan, Raj Krish, Qinyan Pan, Scott Gustafson, Benjamin Kopchick, Laura Opsahl-Ong, Andrea Olvera-Morales, Jonathan Pinney, Kathryn Johnson, Theresa Do, Juergen Klenk, Maria Diaz, Arti Singh, Rong Chai, David A. Clunie, Fred Prior, Keyvan Farahani

arxiv logopreprintJul 31 2025
The de-identification (deID) of protected health information (PHI) and personally identifiable information (PII) is a fundamental requirement for sharing medical images, particularly through public repositories, to ensure compliance with patient privacy laws. In addition, preservation of non-PHI metadata to inform and enable downstream development of imaging artificial intelligence (AI) is an important consideration in biomedical research. The goal of MIDI-B was to provide a standardized platform for benchmarking of DICOM image deID tools based on a set of rules conformant to the HIPAA Safe Harbor regulation, the DICOM Attribute Confidentiality Profiles, and best practices in preservation of research-critical metadata, as defined by The Cancer Imaging Archive (TCIA). The challenge employed a large, diverse, multi-center, and multi-modality set of real de-identified radiology images with synthetic PHI/PII inserted. The MIDI-B Challenge consisted of three phases: training, validation, and test. Eighty individuals registered for the challenge. In the training phase, we encouraged participants to tune their algorithms using their in-house or public data. The validation and test phases utilized the DICOM images containing synthetic identifiers (of 216 and 322 subjects, respectively). Ten teams successfully completed the test phase of the challenge. To measure success of a rule-based approach to image deID, scores were computed as the percentage of correct actions from the total number of required actions. The scores ranged from 97.91% to 99.93%. Participants employed a variety of open-source and proprietary tools with customized configurations, large language models, and optical character recognition (OCR). In this paper we provide a comprehensive report on the MIDI-B Challenge's design, implementation, results, and lessons learned.

SAM-Med3D: A Vision Foundation Model for General-Purpose Segmentation on Volumetric Medical Images.

Wang H, Guo S, Ye J, Deng Z, Cheng J, Li T, Chen J, Su Y, Huang Z, Shen Y, zzzzFu B, Zhang S, He J

pubmed logopapersJul 31 2025
Existing volumetric medical image segmentation models are typically task-specific, excelling at specific targets but struggling to generalize across anatomical structures or modalities. This limitation restricts their broader clinical use. In this article, we introduce segment anything model (SAM)-Med3D, a vision foundation model (VFM) for general-purpose segmentation on volumetric medical images. Given only a few 3-D prompt points, SAM-Med3D can accurately segment diverse anatomical structures and lesions across various modalities. To achieve this, we gather and preprocess a large-scale 3-D medical image segmentation dataset, SA-Med3D-140K, from 70 public datasets and 8K licensed private cases from hospitals. This dataset includes 22K 3-D images and 143K corresponding masks. SAM-Med3D, a promptable segmentation model characterized by its fully learnable 3-D structure, is trained on this dataset using a two-stage procedure and exhibits impressive performance on both seen and unseen segmentation targets. We comprehensively evaluate SAM-Med3D on 16 datasets covering diverse medical scenarios, including different anatomical structures, modalities, targets, and zero-shot transferability to new/unseen tasks. The evaluation demonstrates the efficiency and efficacy of SAM-Med3D, as well as its promising application to diverse downstream tasks as a pretrained model. Our approach illustrates that substantial medical resources can be harnessed to develop a general-purpose medical AI for various potential applications. Our dataset, code, and models are available at: https://github.com/uni-medical/SAM-Med3D.

The evolving role of multimodal imaging, artificial intelligence and radiomics in the radiologic assessment of immune related adverse events.

Das JP, Ma HY, DeJong D, Prendergast C, Baniasadi A, Braumuller B, Giarratana A, Khonji S, Paily J, Shobeiri P, Yeh R, Dercle L, Capaccione KM

pubmed logopapersJul 28 2025
Immunotherapy, in particular checkpoint blockade, has revolutionized the treatment of many advanced cancers. Imaging plays a critical role in assessing both treatment response and the development of immune toxicities. Both conventional imaging and molecular imaging techniques can be used to evaluate multisystemic immune related adverse events (irAEs), including thoracic, abdominal and neurologic irAEs. As artificial intelligence (AI) proliferates in medical imaging, radiologic assessment of irAEs will become more efficient, improving the diagnosis, prognosis, and management of patients affected by immune-related toxicities. This review addresses some of the advancements in medical imaging including the potential future role of radiomics in evaluating irAEs, which may facilitate clinical decision-making and improvements in patient care.

AI-driven preclinical disease risk assessment using imaging in UK biobank.

Seletkov D, Starck S, Mueller TT, Zhang Y, Steinhelfer L, Rueckert D, Braren R

pubmed logopapersJul 26 2025
Identifying disease risk and detecting disease before clinical symptoms appear are essential for early intervention and improving patient outcomes. In this context, the integration of medical imaging in a clinical workflow offers a unique advantage by capturing detailed structural and functional information. Unlike non-image data, such as lifestyle, sociodemographic, or prior medical conditions, which often rely on self-reported information susceptible to recall biases and subjective perceptions, imaging offers more objective and reliable insights. Although the use of medical imaging in artificial intelligence (AI)-driven risk assessment is growing, its full potential remains underutilized. In this work, we demonstrate how imaging can be integrated into routine screening workflows, in particular by taking advantage of neck-to-knee whole-body magnetic resonance imaging (MRI) data available in the large prospective study UK Biobank. Our analysis focuses on three-year risk assessment for a broad spectrum of diseases, including cardiovascular, digestive, metabolic, inflammatory, degenerative, and oncologic conditions. We evaluate AI-based pipelines for processing whole-body MRI and demonstrate that using image-derived radiomics features provides the best prediction performance, interpretability, and integration capability with non-image data.

MedIQA: A Scalable Foundation Model for Prompt-Driven Medical Image Quality Assessment

Siyi Xun, Yue Sun, Jingkun Chen, Zitong Yu, Tong Tong, Xiaohong Liu, Mingxiang Wu, Tao Tan

arxiv logopreprintJul 25 2025
Rapid advances in medical imaging technology underscore the critical need for precise and automated image quality assessment (IQA) to ensure diagnostic accuracy. Existing medical IQA methods, however, struggle to generalize across diverse modalities and clinical scenarios. In response, we introduce MedIQA, the first comprehensive foundation model for medical IQA, designed to handle variability in image dimensions, modalities, anatomical regions, and types. We developed a large-scale multi-modality dataset with plentiful manually annotated quality scores to support this. Our model integrates a salient slice assessment module to focus on diagnostically relevant regions feature retrieval and employs an automatic prompt strategy that aligns upstream physical parameter pre-training with downstream expert annotation fine-tuning. Extensive experiments demonstrate that MedIQA significantly outperforms baselines in multiple downstream tasks, establishing a scalable framework for medical IQA and advancing diagnostic workflows and clinical decision-making.

Artificial intelligence in radiology: 173 commercially available products and their scientific evidence.

Antonissen N, Tryfonos O, Houben IB, Jacobs C, de Rooij M, van Leeuwen KG

pubmed logopapersJul 24 2025
To assess changes in peer-reviewed evidence on commercially available radiological artificial intelligence (AI) products from 2020 to 2023, as a follow-up to a 2020 review of 100 products. A literature review was conducted, covering January 2015 to March 2023, focusing on CE-certified radiological AI products listed on www.healthairegister.com . Papers were categorised using the hierarchical model of efficacy: technical/diagnostic accuracy (levels 1-2), clinical decision-making and patient outcomes (levels 3-5), or socio-economic impact (level 6). Study features such as design, vendor independence, and multicentre/multinational data usage were also examined. By 2023, 173 CE-certified AI products from 90 vendors were identified, compared to 100 products in 2020. Products with peer-reviewed evidence increased from 36% to 66%, supported by 639 papers (up from 237). Diagnostic accuracy studies (level 2) remained predominant, though their share decreased from 65% to 57%. Studies addressing higher-efficacy levels (3-6) remained constant at 22% and 24%, with the number of products supported by such evidence increasing from 18% to 31%. Multicentre studies rose from 30% to 41% (p < 0.01). However, vendor-independent studies decreased (49% to 45%), as did multinational studies (15% to 11%) and prospective designs (19% to 16%), all with p > 0.05. The increase in peer-reviewed evidence and higher levels of evidence per product indicate maturation in the radiological AI market. However, the continued focus on lower-efficacy studies and reductions in vendor independence, multinational data, and prospective designs highlight persistent challenges in establishing unbiased, real-world evidence. Question Evaluating advancements in peer-reviewed evidence for CE-certified radiological AI products is crucial to understand their clinical adoption and impact. Findings CE-certified AI products with peer-reviewed evidence increased from 36% in 2020 to 66% in 2023, but the proportion of higher-level evidence papers (~24%) remained unchanged. Clinical relevance The study highlights increased validation of radiological AI products but underscores a continued lack of evidence on their clinical and socio-economic impact, which may limit these tools' safe and effective implementation into clinical workflows.

A Tutorial on MRI Reconstruction: From Modern Methods to Clinical Implications

Tolga Çukur, Salman U. H. Dar, Valiyeh Ansarian Nezhad, Yohan Jun, Tae Hyung Kim, Shohei Fujita, Berkin Bilgic

arxiv logopreprintJul 22 2025
MRI is an indispensable clinical tool, offering a rich variety of tissue contrasts to support broad diagnostic and research applications. Clinical exams routinely acquire multiple structural sequences that provide complementary information for differential diagnosis, while research protocols often incorporate advanced functional, diffusion, spectroscopic, and relaxometry sequences to capture multidimensional insights into tissue structure and composition. However, these capabilities come at the cost of prolonged scan times, which reduce patient throughput, increase susceptibility to motion artifacts, and may require trade-offs in image quality or diagnostic scope. Over the last two decades, advances in image reconstruction algorithms--alongside improvements in hardware and pulse sequence design--have made it possible to accelerate acquisitions while preserving diagnostic quality. Central to this progress is the ability to incorporate prior information to regularize the solutions to the reconstruction problem. In this tutorial, we overview the basics of MRI reconstruction and highlight state-of-the-art approaches, beginning with classical methods that rely on explicit hand-crafted priors, and then turning to deep learning methods that leverage a combination of learned and crafted priors to further push the performance envelope. We also explore the translational aspects and eventual clinical implications of these methods. We conclude by discussing future directions to address remaining challenges in MRI reconstruction. The tutorial is accompanied by a Python toolbox (https://github.com/tutorial-MRI-recon/tutorial) to demonstrate select methods discussed in the article.

MLRU++: Multiscale Lightweight Residual UNETR++ with Attention for Efficient 3D Medical Image Segmentation

Nand Kumar Yadav, Rodrigue Rizk, William CW Chen, KC Santosh

arxiv logopreprintJul 22 2025
Accurate and efficient medical image segmentation is crucial but challenging due to anatomical variability and high computational demands on volumetric data. Recent hybrid CNN-Transformer architectures achieve state-of-the-art results but add significant complexity. In this paper, we propose MLRU++, a Multiscale Lightweight Residual UNETR++ architecture designed to balance segmentation accuracy and computational efficiency. It introduces two key innovations: a Lightweight Channel and Bottleneck Attention Module (LCBAM) that enhances contextual feature encoding with minimal overhead, and a Multiscale Bottleneck Block (M2B) in the decoder that captures fine-grained details via multi-resolution feature aggregation. Experiments on four publicly available benchmark datasets (Synapse, BTCV, ACDC, and Decathlon Lung) demonstrate that MLRU++ achieves state-of-the-art performance, with average Dice scores of 87.57% (Synapse), 93.00% (ACDC), and 81.12% (Lung). Compared to existing leading models, MLRU++ improves Dice scores by 5.38% and 2.12% on Synapse and ACDC, respectively, while significantly reducing parameter count and computational cost. Ablation studies evaluating LCBAM and M2B further confirm the effectiveness of the proposed architectural components. Results suggest that MLRU++ offers a practical and high-performing solution for 3D medical image segmentation tasks. Source code is available at: https://github.com/1027865/MLRUPP
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