Daily Papers

Magnetic resonance imaging (MRI) is a central modality for stroke imaging. It is used upon patient admission to make treatment decisions such as selecting patients for intravenous thrombolysis or endovascular therapy. MRI is later used in the duration of hospital stay to predict outcome by visualizing infarct core size and location. Furthermore, it may be used to characterize stroke etiology, e.g. differentiation between (cardio)-embolic and non-embolic stroke. Computer based automated medical image processing is increasingly finding its way into clinical routine. Previous iterations of the Ischemic Stroke Lesion Segmentation (ISLES) challenge have aided in the generation of identifying benchmark methods for acute and sub-acute ischemic stroke lesion segmentation. Here we introduce an expert-annotated, multicenter MRI dataset for segmentation of acute to subacute stroke lesions. This dataset comprises 400 multi-vendor MRI cases with high variability in stroke lesion size, quantity and location. It is split into a training dataset of n=250 and a test dataset of n=150. All training data will be made publicly available. The test dataset will be used for model validation only and will not be released to the public. This dataset serves as the foundation of the ISLES 2022 challenge with the goal of finding algorithmic methods to enable the development and benchmarking of robust and accurate segmentation algorithms for ischemic stroke.

Diffusion Magnetic Resonance Imaging (dMRI) plays a crucial role in the noninvasive investigation of tissue microstructural properties and structural connectivity in the in vivo human brain. However, to effectively capture the intricate characteristics of water diffusion at various directions and scales, it is important to employ comprehensive q-space sampling. Unfortunately, this requirement leads to long scan times, limiting the clinical applicability of dMRI. To address this challenge, we propose SSOR, a Simultaneous q-Space sampling Optimization and Reconstruction framework. We jointly optimize a subset of q-space samples using a continuous representation of spherical harmonic functions and a reconstruction network. Additionally, we integrate the unique properties of diffusion magnetic resonance imaging (dMRI) in both the q-space and image domains by applying l1-norm and total-variation regularization. The experiments conducted on HCP data demonstrate that SSOR has promising strengths both quantitatively and qualitatively and exhibits robustness to noise.

We present FOMO60K, a large-scale, heterogeneous dataset of 60,529 brain Magnetic Resonance Imaging (MRI) scans from 13,900 sessions and 11,187 subjects, aggregated from 16 publicly available sources. The dataset includes both clinical- and research-grade images, multiple MRI sequences, and a wide range of anatomical and pathological variability, including scans with large brain anomalies. Minimal preprocessing was applied to preserve the original image characteristics while reducing barriers to entry for new users. Accompanying code for self-supervised pretraining and finetuning is provided. FOMO60K is intended to support the development and benchmarking of self-supervised learning methods in medical imaging at scale.

Learning based single image super resolution (SISR) task is well investigated in 2D images. However, SISR for 3D Magnetics Resonance Images (MRI) is more challenging compared to 2D, mainly due to the increased number of neural network parameters, the larger memory requirement and the limited amount of available training data. Current SISR methods for 3D volumetric images are based on Generative Adversarial Networks (GANs), especially Wasserstein GANs due to their training stability. Other common architectures in the 2D domain, e.g. transformer models, require large amounts of training data and are therefore not suitable for the limited 3D data. However, Wasserstein GANs can be problematic because they may not converge to a global optimum and thus produce blurry results. Here, we propose a new method for 3D SR based on the GAN framework. Specifically, we use instance noise to balance the GAN training. Furthermore, we use a relativistic GAN loss function and an updating feature extractor during the training process. We show that our method produces highly accurate results. We also show that we need very few training samples. In particular, we need less than 30 samples instead of thousands of training samples that are typically required in previous studies. Finally, we show improved out-of-sample results produced by our model.

AI is revolutionizing MRI along the acquisition and processing chain. Advanced AI frameworks have been developed to apply AI in various successive tasks, such as image reconstruction, quantitative parameter map estimation, and image segmentation. Existing frameworks are often designed to perform tasks independently or are focused on specific models or datasets, limiting generalization. We introduce ATOMMIC, an open-source toolbox that streamlines AI applications for accelerated MRI reconstruction and analysis. ATOMMIC implements several tasks using DL networks and enables MultiTask Learning (MTL) to perform related tasks integrated, targeting generalization in the MRI domain. We first review the current state of AI frameworks for MRI through a comprehensive literature search and by parsing 12,479 GitHub repositories. We benchmark 25 DL models on eight publicly available datasets to present distinct applications of ATOMMIC on accelerated MRI reconstruction, image segmentation, quantitative parameter map estimation, and joint accelerated MRI reconstruction and image segmentation utilizing MTL. Our findings demonstrate that ATOMMIC is the only MTL framework with harmonized complex-valued and real-valued data support. Evaluations on single tasks show that physics-based models, which enforce data consistency by leveraging the physical properties of MRI, outperform other models in reconstructing highly accelerated acquisitions. Physics-based models that produce high reconstruction quality can accurately estimate quantitative parameter maps. When high-performing reconstruction models are combined with robust segmentation networks utilizing MTL, performance is improved in both tasks. ATOMMIC facilitates MRI reconstruction and analysis by standardizing workflows, enhancing data interoperability, integrating unique features like MTL, and effectively benchmarking DL models.

Most papers caution against using predictive models for disease stratification based on unselected radiomic features, as these features are affected by contouring variability. Instead, they advocate for the use of the Intraclass Correlation Coefficient (ICC) as a measure of stability for feature selection. However, the direct effect of segmentation variability on the predictive models is rarely studied. This study investigates the impact of segmentation variability on feature stability and predictive performance in radiomics-based prediction of Triple-Negative Breast Cancer (TNBC) subtype using Magnetic Resonance Imaging. A total of 244 images from the Duke dataset were used, with segmentation variability introduced through modifications of manual segmentations. For each mask, explainable radiomic features were selected using the Shapley Additive exPlanations method and used to train logistic regression models. Feature stability across segmentations was assessed via ICC, Pearson's correlation, and reliability scores quantifying the relationship between feature stability and segmentation variability. Results indicate that segmentation accuracy does not significantly impact predictive performance. While incorporating peritumoral information may reduce feature reproducibility, it does not diminish feature predictive capability. Moreover, feature selection in predictive models is not inherently tied to feature stability with respect to segmentation, suggesting that an overreliance on ICC or reliability scores for feature selection might exclude valuable predictive features.

We propose a novel neural deformable model (NDM) targeting at the reconstruction and modeling of 3D bi-ventricular shape of the heart from 2D sparse cardiac magnetic resonance (CMR) imaging data. We model the bi-ventricular shape using blended deformable superquadrics, which are parameterized by a set of geometric parameter functions and are capable of deforming globally and locally. While global geometric parameter functions and deformations capture gross shape features from visual data, local deformations, parameterized as neural diffeomorphic point flows, can be learned to recover the detailed heart shape.Different from iterative optimization methods used in conventional deformable model formulations, NDMs can be trained to learn such geometric parameter functions, global and local deformations from a shape distribution manifold. Our NDM can learn to densify a sparse cardiac point cloud with arbitrary scales and generate high-quality triangular meshes automatically. It also enables the implicit learning of dense correspondences among different heart shape instances for accurate cardiac shape registration. Furthermore, the parameters of NDM are intuitive, and can be used by a physician without sophisticated post-processing. Experimental results on a large CMR dataset demonstrate the improved performance of NDM over conventional methods.

Magnetic resonance imaging (MRI) is a crucial tool to identify brain abnormalities in a wide range of neurological disorders. In focal epilepsy MRI is used to identify structural cerebral abnormalities. For covert lesions, machine learning and artificial intelligence algorithms may improve lesion detection if abnormalities are not evident on visual inspection. The success of this approach depends on the volume and quality of training data. Herein, we release an open-source dataset of preprocessed MRI scans from 442 individuals with drug-refractory focal epilepsy who had neurosurgical resections, and detailed demographic information. The MRI scan data includes the preoperative 3D T1 and where available 3D FLAIR, as well as a manually inspected complete surface reconstruction and volumetric parcellations. Demographic information includes age, sex, age of onset of epilepsy, location of surgery, histopathology of resected specimen, occurrence and frequency of focal seizures with and without impairment of awareness, focal to bilateral tonic-clonic seizures, number of anti-seizure medications (ASMs) at time of surgery, and a total of 1764 patient years of post-surgical follow up. Crucially, we also include resection masks delineated from post-surgical imaging. To demonstrate the veracity of our data, we successfully replicated previous studies showing long-term outcomes of seizure freedom in the range of around 50%. Our imaging data replicates findings of group level atrophy in patients compared to controls. Resection locations in the cohort were predominantly in the temporal and frontal lobes. We envisage our dataset, shared openly with the community, will catalyse the development and application of computational methods in clinical neurology.

Off-resonance artifacts in magnetic resonance imaging (MRI) are visual distortions that occur when the actual resonant frequencies of spins within the imaging volume differ from the expected frequencies used to encode spatial information. These discrepancies can be caused by a variety of factors, including magnetic field inhomogeneities, chemical shifts, or susceptibility differences within the tissues. Such artifacts can manifest as blurring, ghosting, or misregistration of the reconstructed image, and they often compromise its diagnostic quality. We propose to resolve these artifacts by lifting the 2D MRI reconstruction problem to 3D, introducing an additional "spectral" dimension to model this off-resonance. Our approach is inspired by recent progress in modeling radiance fields, and is capable of reconstructing both static and dynamic MR images as well as separating fat and water, which is of independent clinical interest. We demonstrate our approach in the context of PROPELLER (Periodically Rotated Overlapping ParallEL Lines with Enhanced Reconstruction) MRI acquisitions, which are popular for their robustness to motion artifacts. Our method operates in a few minutes on a single GPU, and to our knowledge is the first to correct for chemical shift in gradient echo PROPELLER MRI reconstruction without additional measurements or pretraining data.

The recent introduction of synthetic correlated diffusion (CDI^s) imaging has demonstrated significant potential in the realm of clinical decision support for prostate cancer (PCa). CDI^s is a new form of magnetic resonance imaging (MRI) designed to characterize tissue characteristics through the joint correlation of diffusion signal attenuation across different Brownian motion sensitivities. Despite the performance improvement, the CDI^s data for PCa has not been previously made publicly available. In our commitment to advance research efforts for PCa, we introduce Cancer-Net PCa-Data, an open-source benchmark dataset of volumetric CDI^s imaging data of PCa patients. Cancer-Net PCa-Data consists of CDI^s volumetric images from a patient cohort of 200 patient cases, along with full annotations (gland masks, tumor masks, and PCa diagnosis for each tumor). We also analyze the demographic and label region diversity of Cancer-Net PCa-Data for potential biases. Cancer-Net PCa-Data is the first-ever public dataset of CDI^s imaging data for PCa, and is a part of the global open-source initiative dedicated to advancement in machine learning and imaging research to aid clinicians in the global fight against cancer.

Intravascular ultrasound (IVUS) offers a unique perspective in the treatment of vascular diseases by creating a sequence of ultrasound-slices acquired from within the vessel. However, unlike conventional hand-held ultrasound, the thin catheter only provides room for a small number of physical channels for signal transfer from a transducer-array at the tip. For continued improvement of image quality and frame rate, we present the use of deep reinforcement learning to deal with the current physical information bottleneck. Valuable inspiration has come from the field of magnetic resonance imaging (MRI), where learned acquisition schemes have brought significant acceleration in image acquisition at competing image quality. To efficiently accelerate IVUS imaging, we propose a framework that utilizes deep reinforcement learning for an optimal adaptive acquisition policy on a per-frame basis enabled by actor-critic methods and Gumbel top-K sampling.

The diffusion MRI Neurite Exchange Imaging model offers a promising framework for probing gray matter microstructure by estimating parameters such as compartment sizes, diffusivities, and inter-compartmental water exchange time. However, existing protocols require long scan times. This study proposes a reduced acquisition scheme for the Connectome 2.0 scanner that preserves model accuracy while substantially shortening scan duration. We developed a data-driven framework using explainable artificial intelligence with a guided recursive feature elimination strategy to identify an optimal 8-feature subset from a 15-feature protocol. The performance of this optimized protocol was validated in vivo and benchmarked against the full acquisition and alternative reduction strategies. Parameter accuracy, preservation of anatomical contrast, and test-retest reproducibility were assessed. The reduced protocol yielded parameter estimates and cortical maps comparable to the full protocol, with low estimation errors in synthetic data and minimal impact on test-retest variability. Compared to theory-driven and heuristic reduction schemes, the optimized protocol demonstrated superior robustness, reducing the deviation in water exchange time estimates by over two-fold. In conclusion, this hybrid optimization framework enables viable imaging of neurite exchange in 14 minutes without loss of parameter fidelity. This approach supports the broader application of exchange-sensitive diffusion magnetic resonance imaging in neuroscience and clinical research, and offers a generalizable method for designing efficient acquisition protocols in biophysical parameter mapping.

This paper presents a data-driven, task-specific paradigm for experimental design, to shorten acquisition time, reduce costs, and accelerate the deployment of imaging devices. Current approaches in experimental design focus on model-parameter estimation and require specification of a particular model, whereas in imaging, other tasks may drive the design. Furthermore, such approaches often lead to intractable optimization problems in real-world imaging applications. Here we present a new paradigm for experimental design that simultaneously optimizes the design (set of image channels) and trains a machine-learning model to execute a user-specified image-analysis task. The approach obtains data densely-sampled over the measurement space (many image channels) for a small number of acquisitions, then identifies a subset of channels of prespecified size that best supports the task. We propose a method: TADRED for TAsk-DRiven Experimental Design in imaging, to identify the most informative channel-subset whilst simultaneously training a network to execute the task given the subset. Experiments demonstrate the potential of TADRED in diverse imaging applications: several clinically-relevant tasks in magnetic resonance imaging; and remote sensing and physiological applications of hyperspectral imaging. Results show substantial improvement over classical experimental design, two recent application-specific methods within the new paradigm, and state-of-the-art approaches in supervised feature selection. We anticipate further applications of our approach. Code is available: https://github.com/sbb-gh/experimental-design-multichannel

Reconstructing medical images from partial measurements is an important inverse problem in Computed Tomography (CT) and Magnetic Resonance Imaging (MRI). Existing solutions based on machine learning typically train a model to directly map measurements to medical images, leveraging a training dataset of paired images and measurements. These measurements are typically synthesized from images using a fixed physical model of the measurement process, which hinders the generalization capability of models to unknown measurement processes. To address this issue, we propose a fully unsupervised technique for inverse problem solving, leveraging the recently introduced score-based generative models. Specifically, we first train a score-based generative model on medical images to capture their prior distribution. Given measurements and a physical model of the measurement process at test time, we introduce a sampling method to reconstruct an image consistent with both the prior and the observed measurements. Our method does not assume a fixed measurement process during training, and can thus be flexibly adapted to different measurement processes at test time. Empirically, we observe comparable or better performance to supervised learning techniques in several medical imaging tasks in CT and MRI, while demonstrating significantly better generalization to unknown measurement processes.

Most existing learning-based methods for solving imaging inverse problems can be roughly divided into two classes: iterative algorithms, such as plug-and-play and diffusion methods, that leverage pretrained denoisers, and unrolled architectures that are trained end-to-end for specific imaging problems. Iterative methods in the first class are computationally costly and often provide suboptimal reconstruction performance, whereas unrolled architectures are generally specific to a single inverse problem and require expensive training. In this work, we propose a novel non-iterative, lightweight architecture that incorporates knowledge about the forward operator (acquisition physics and noise parameters) without relying on unrolling. Our model is trained to solve a wide range of inverse problems beyond denoising, including deblurring, magnetic resonance imaging, computed tomography, inpainting, and super-resolution. The proposed model can be easily adapted to unseen inverse problems or datasets with a few fine-tuning steps (up to a few images) in a self-supervised way, without ground-truth references. Throughout a series of experiments, we demonstrate state-of-the-art performance from medical imaging to low-photon imaging and microscopy.

This paper presents an annotated dataset of brain MRI images designed to advance the field of brain symmetry study. Magnetic resonance imaging (MRI) has gained interest in analyzing brain symmetry in neonatal infants, and challenges remain due to the vast size differences between fetal and adult brains. Classification methods for brain structural MRI use scales and visual cues to assess hemisphere symmetry, which can help diagnose neonatal patients by comparing hemispheres and anatomical regions of interest in the brain. Using the Developing Human Connectome Project dataset, this work presents a dataset comprising cerebral images extracted as slices across selected portions of interest for clinical evaluation . All the extracted images are annotated with the brain's midline. All the extracted images are annotated with the brain's midline. From the assumption that a decrease in symmetry is directly related to possible clinical pathologies, the dataset can contribute to a more precise diagnosis because it can be used to train deep learning model application in neonatal cerebral MRI anomaly detection from postnatal infant scans thanks to computer vision. Such models learn to identify and classify anomalies by identifying potential asymmetrical patterns in medical MRI images. Furthermore, this dataset can contribute to the research and development of methods using the relative symmetry of the two brain hemispheres for crucial diagnosis and treatment planning.

Radiation therapy plays a crucial role in cancer treatment, necessitating precise delivery of radiation to tumors while sparing healthy tissues over multiple days. Computed tomography (CT) is integral for treatment planning, offering electron density data crucial for accurate dose calculations. However, accurately representing patient anatomy is challenging, especially in adaptive radiotherapy, where CT is not acquired daily. Magnetic resonance imaging (MRI) provides superior soft-tissue contrast. Still, it lacks electron density information while cone beam CT (CBCT) lacks direct electron density calibration and is mainly used for patient positioning. Adopting MRI-only or CBCT-based adaptive radiotherapy eliminates the need for CT planning but presents challenges. Synthetic CT (sCT) generation techniques aim to address these challenges by using image synthesis to bridge the gap between MRI, CBCT, and CT. The SynthRAD2023 challenge was organized to compare synthetic CT generation methods using multi-center ground truth data from 1080 patients, divided into two tasks: 1) MRI-to-CT and 2) CBCT-to-CT. The evaluation included image similarity and dose-based metrics from proton and photon plans. The challenge attracted significant participation, with 617 registrations and 22/17 valid submissions for tasks 1/2. Top-performing teams achieved high structural similarity indices (>0.87/0.90) and gamma pass rates for photon (>98.1%/99.0%) and proton (>99.0%/97.3%) plans. However, no significant correlation was found between image similarity metrics and dose accuracy, emphasizing the need for dose evaluation when assessing the clinical applicability of sCT. SynthRAD2023 facilitated the investigation and benchmarking of sCT generation techniques, providing insights for developing MRI-only and CBCT-based adaptive radiotherapy.

Magnetic Resonance Imaging with tagging (tMRI) has long been utilized for quantifying tissue motion and strain during deformation. However, a phenomenon known as tag fading, a gradual decrease in tag visibility over time, often complicates post-processing. The first contribution of this study is to model tag fading by considering the interplay between T_1 relaxation and the repeated application of radio frequency (RF) pulses during serial imaging sequences. This is a factor that has been overlooked in prior research on tMRI post-processing. Further, we have observed an emerging trend of utilizing raw tagged MRI within a deep learning-based (DL) registration framework for motion estimation. In this work, we evaluate and analyze the impact of commonly used image similarity objectives in training DL registrations on raw tMRI. This is then compared with the Harmonic Phase-based approach, a traditional approach which is claimed to be robust to tag fading. Our findings, derived from both simulated images and an actual phantom scan, reveal the limitations of various similarity losses in raw tMRI and emphasize caution in registration tasks where image intensity changes over time.

Magnetic Resonance Imaging (MRI) is a critical tool in modern medical diagnostics, yet its prolonged acquisition time remains a critical limitation, especially in time-sensitive clinical scenarios. While undersampling strategies can accelerate image acquisition, they often result in image artifacts and degraded quality. Recent diffusion models have shown promise for reconstructing high-fidelity images from undersampled data by learning powerful image priors; however, most existing approaches either (i) rely on unsupervised score functions without paired supervision or (ii) apply data consistency only as a post-processing step. In this work, we introduce a conditional denoising diffusion framework with iterative data-consistency correction, which differs from prior methods by embedding the measurement model directly into every reverse diffusion step and training the model on paired undersampled-ground truth data. This hybrid design bridges generative flexibility with explicit enforcement of MRI physics. Experiments on the fastMRI dataset demonstrate that our framework consistently outperforms recent state-of-the-art deep learning and diffusion-based methods in SSIM, PSNR, and LPIPS, with LPIPS capturing perceptual improvements more faithfully. These results demonstrate that integrating conditional supervision with iterative consistency updates yields substantial improvements in both pixel-level fidelity and perceptual realism, establishing a principled and practical advance toward robust, accelerated MRI reconstruction.

Magnetic Resonance Imaging (MRI), including diffusion MRI (dMRI), serves as a ``microscope'' for anatomical structures and routinely mitigates the influence of low signal-to-noise ratio scans by compromising temporal or spatial resolution. However, these compromises fail to meet clinical demands for both efficiency and precision. Consequently, denoising is a vital preprocessing step, particularly for dMRI, where clean data is unavailable. In this paper, we introduce Di-Fusion, a fully self-supervised denoising method that leverages the latter diffusion steps and an adaptive sampling process. Unlike previous approaches, our single-stage framework achieves efficient and stable training without extra noise model training and offers adaptive and controllable results in the sampling process. Our thorough experiments on real and simulated data demonstrate that Di-Fusion achieves state-of-the-art performance in microstructure modeling, tractography tracking, and other downstream tasks. Code is available at https://github.com/FouierL/Di-Fusion.

Magnetic resonance imaging (MRI) is the standard modality to understand human brain structure and function in vivo (antemortem). Decades of research in human neuroimaging has led to the widespread development of methods and tools to provide automated volume-based segmentations and surface-based parcellations which help localize brain functions to specialized anatomical regions. Recently ex vivo (postmortem) imaging of the brain has opened-up avenues to study brain structure at sub-millimeter ultra high-resolution revealing details not possible to observe with in vivo MRI. Unfortunately, there has been limited methodological development in ex vivo MRI primarily due to lack of datasets and limited centers with such imaging resources. Therefore, in this work, we present one-of-its-kind dataset of 82 ex vivo T2w whole brain hemispheres MRI at 0.3 mm isotropic resolution spanning Alzheimer's disease and related dementias. We adapted and developed a fast and easy-to-use automated surface-based pipeline to parcellate, for the first time, ultra high-resolution ex vivo brain tissue at the native subject space resolution using the Desikan-Killiany-Tourville (DKT) brain atlas. This allows us to perform vertex-wise analysis in the template space and thereby link morphometry measures with pathology measurements derived from histology. We will open-source our dataset docker container, Jupyter notebooks for ready-to-use out-of-the-box set of tools and command line options to advance ex vivo MRI clinical brain imaging research on the project webpage.

Magnetic resonance imaging (MRI) is a common and life-saving medical imaging technique. However, acquiring high signal-to-noise ratio MRI scans requires long scan times, resulting in increased costs and patient discomfort, and decreased throughput. Thus, there is great interest in denoising MRI scans, especially for the subtype of diffusion MRI scans that are severely SNR-limited. While most prior MRI denoising methods are supervised in nature, acquiring supervised training datasets for the multitude of anatomies, MRI scanners, and scan parameters proves impractical. Here, we propose Denoising Diffusion Models for Denoising Diffusion MRI (DDM^2), a self-supervised denoising method for MRI denoising using diffusion denoising generative models. Our three-stage framework integrates statistic-based denoising theory into diffusion models and performs denoising through conditional generation. During inference, we represent input noisy measurements as a sample from an intermediate posterior distribution within the diffusion Markov chain. We conduct experiments on 4 real-world in-vivo diffusion MRI datasets and show that our DDM^2 demonstrates superior denoising performances ascertained with clinically-relevant visual qualitative and quantitative metrics.

Magnetic resonance imaging (MRI) is a cornerstone of modern medical imaging. However, long image acquisition times, the need for qualitative expert analysis, and the lack of (and difficulty extracting) quantitative indicators that are sensitive to tissue health have curtailed widespread clinical and research studies. While recent machine learning methods for MRI reconstruction and analysis have shown promise for reducing this burden, these techniques are primarily validated with imperfect image quality metrics, which are discordant with clinically-relevant measures that ultimately hamper clinical deployment and clinician trust. To mitigate this challenge, we present the Stanford Knee MRI with Multi-Task Evaluation (SKM-TEA) dataset, a collection of quantitative knee MRI (qMRI) scans that enables end-to-end, clinically-relevant evaluation of MRI reconstruction and analysis tools. This 1.6TB dataset consists of raw-data measurements of ~25,000 slices (155 patients) of anonymized patient MRI scans, the corresponding scanner-generated DICOM images, manual segmentations of four tissues, and bounding box annotations for sixteen clinically relevant pathologies. We provide a framework for using qMRI parameter maps, along with image reconstructions and dense image labels, for measuring the quality of qMRI biomarker estimates extracted from MRI reconstruction, segmentation, and detection techniques. Finally, we use this framework to benchmark state-of-the-art baselines on this dataset. We hope our SKM-TEA dataset and code can enable a broad spectrum of research for modular image reconstruction and image analysis in a clinically informed manner. Dataset access, code, and benchmarks are available at https://github.com/StanfordMIMI/skm-tea.

Magnetic resonance imaging (MRI) provides high spatial resolution and excellent soft-tissue contrast without using harmful ionising radiation. Dynamic MRI is an essential tool for interventions to visualise movements or changes of the target organ. However, such MRI acquisition with high temporal resolution suffers from limited spatial resolution - also known as the spatio-temporal trade-off of dynamic MRI. Several approaches, including deep learning based super-resolution approaches, have been proposed to mitigate this trade-off. Nevertheless, such an approach typically aims to super-resolve each time-point separately, treating them as individual volumes. This research addresses the problem by creating a deep learning model which attempts to learn both spatial and temporal relationships. A modified 3D UNet model, DDoS-UNet, is proposed - which takes the low-resolution volume of the current time-point along with a prior image volume. Initially, the network is supplied with a static high-resolution planning scan as the prior image along with the low-resolution input to super-resolve the first time-point. Then it continues step-wise by using the super-resolved time-points as the prior image while super-resolving the subsequent time-points. The model performance was tested with 3D dynamic data that was undersampled to different in-plane levels. The proposed network achieved an average SSIM value of 0.951pm0.017 while reconstructing the lowest resolution data (i.e. only 4\% of the k-space acquired) - which could result in a theoretical acceleration factor of 25. The proposed approach can be used to reduce the required scan-time while achieving high spatial resolution.

Magnetic Resonance Imaging can produce detailed images of the anatomy and physiology of the human body that can assist doctors in diagnosing and treating pathologies such as tumours. However, MRI suffers from very long acquisition times that make it susceptible to patient motion artifacts and limit its potential to deliver dynamic treatments. Conventional approaches such as Parallel Imaging and Compressed Sensing allow for an increase in MRI acquisition speed by reconstructing MR images from sub-sampled MRI data acquired using multiple receiver coils. Recent advancements in Deep Learning combined with Parallel Imaging and Compressed Sensing techniques have the potential to produce high-fidelity reconstructions from highly accelerated MRI data. In this work we present a novel Deep Learning-based Inverse Problem solver applied to the task of Accelerated MRI Reconstruction, called the Recurrent Variational Network (RecurrentVarNet), by exploiting the properties of Convolutional Recurrent Neural Networks and unrolled algorithms for solving Inverse Problems. The RecurrentVarNet consists of multiple recurrent blocks, each responsible for one iteration of the unrolled variational optimization scheme for solving the inverse problem of multi-coil Accelerated MRI Reconstruction. Contrary to traditional approaches, the optimization steps are performed in the observation domain (k-space) instead of the image domain. Each block of the RecurrentVarNet refines the observed k-space and comprises a data consistency term and a recurrent unit which takes as input a learned hidden state and the prediction of the previous block. Our proposed method achieves new state of the art qualitative and quantitative reconstruction results on 5-fold and 10-fold accelerated data from a public multi-coil brain dataset, outperforming previous conventional and deep learning-based approaches.

Diffusion-weighted magnetic resonance imaging (DW-MRI) can be used to characterise the microstructure of the nervous tissue, e.g. to delineate brain white matter connections in a non-invasive manner via fibre tracking. Magnetic Resonance Imaging (MRI) in high spatial resolution would play an important role in visualising such fibre tracts in a superior manner. However, obtaining an image of such resolution comes at the expense of longer scan time. Longer scan time can be associated with the increase of motion artefacts, due to the patient's psychological and physical conditions. Single Image Super-Resolution (SISR), a technique aimed to obtain high-resolution (HR) details from one single low-resolution (LR) input image, achieved with Deep Learning, is the focus of this study. Compared to interpolation techniques or sparse-coding algorithms, deep learning extracts prior knowledge from big datasets and produces superior MRI images from the low-resolution counterparts. In this research, a deep learning based super-resolution technique is proposed and has been applied for DW-MRI. Images from the IXI dataset have been used as the ground-truth and were artificially downsampled to simulate the low-resolution images. The proposed method has shown statistically significant improvement over the baselines and achieved an SSIM of 0.913pm0.045.

Magnetic Resonance Imaging (MRI) is a widely-accepted imaging technique for knee injury analysis. Its advantage of capturing knee structure in three dimensions makes it the ideal tool for radiologists to locate potential tears in the knee. In order to better confront the ever growing workload of musculoskeletal (MSK) radiologists, automated tools for patients' triage are becoming a real need, reducing delays in the reading of pathological cases. In this work, we present the Efficiently-Layered Network (ELNet), a convolutional neural network (CNN) architecture optimized for the task of initial knee MRI diagnosis for triage. Unlike past approaches, we train ELNet from scratch instead of using a transfer-learning approach. The proposed method is validated quantitatively and qualitatively, and compares favorably against state-of-the-art MRNet while using a single imaging stack (axial or coronal) as input. Additionally, we demonstrate our model's capability to locate tears in the knee despite the absence of localization information during training. Lastly, the proposed model is extremely lightweight (< 1MB) and therefore easy to train and deploy in real clinical settings. The code for our model is provided at: https://github.com/mxtsai/ELNet.

Multiparametric magnetic resonance imaging (mpMRI) has demonstrated promising results in prostate cancer (PCa) detection using deep convolutional neural networks (CNNs). Recently, transformers have achieved competitive performance compared to CNNs in computer vision. Large-scale transformers need abundant annotated data for training, which are difficult to obtain in medical imaging. Self-supervised learning can effectively leverage unlabeled data to extract useful semantic representations without annotation and its associated costs. This can improve model performance on downstream tasks with limited labelled data and increase generalizability. We introduce a novel end-to-end Cross-Shaped windows (CSwin) transformer UNet model, CSwin UNet, to detect clinically significant prostate cancer (csPCa) in prostate bi-parametric MR imaging (bpMRI) and demonstrate the effectiveness of our proposed self-supervised pre-training framework. Using a large prostate bpMRI dataset with 1500 patients, we first pre-train CSwin transformer using multi-task self-supervised learning to improve data-efficiency and network generalizability. We then finetuned using lesion annotations to perform csPCa detection. Five-fold cross validation shows that self-supervised CSwin UNet achieves 0.888 AUC and 0.545 Average Precision (AP), significantly outperforming four state-of-the-art models (Swin UNETR, DynUNet, Attention UNet, UNet). Using a separate bpMRI dataset with 158 patients, we evaluated our model robustness to external hold-out data. Self-supervised CSwin UNet achieves 0.79 AUC and 0.45 AP, still outperforming all other comparable methods and demonstrating generalization to a dataset shift.

Tagged magnetic resonance imaging (tMRI) has been employed for decades to measure the motion of tissue undergoing deformation. However, registration-based motion estimation from tMRI is difficult due to the periodic patterns in these images, particularly when the motion is large. With a larger motion the registration approach gets trapped in a local optima, leading to motion estimation errors. We introduce a novel "momenta, shooting, and correction" framework for Lagrangian motion estimation in the presence of repetitive patterns and large motion. This framework, grounded in Lie algebra and Lie group principles, accumulates momenta in the tangent vector space and employs exponential mapping in the diffeomorphic space for rapid approximation towards true optima, circumventing local optima. A subsequent correction step ensures convergence to true optima. The results on a 2D synthetic dataset and a real 3D tMRI dataset demonstrate our method's efficiency in estimating accurate, dense, and diffeomorphic 2D/3D motion fields amidst large motion and repetitive patterns.

Multimodal magnetic resonance imaging (MRI) constitutes the first line of investigation for clinicians in the care of brain tumors, providing crucial insights for surgery planning, treatment monitoring, and biomarker identification. Pre-training on large datasets have been shown to help models learn transferable representations and adapt with minimal labeled data. This behavior is especially valuable in medical imaging, where annotations are often scarce. However, applying this paradigm to multimodal medical data introduces a challenge: most existing approaches assume that all imaging modalities are available during both pre-training and fine-tuning. In practice, missing modalities often occur due to acquisition issues, specialist unavailability, or specific experimental designs on small in-house datasets. Consequently, a common approach involves training a separate model for each desired modality combination, making the process both resource-intensive and impractical for clinical use. Therefore, we introduce BM-MAE, a masked image modeling pre-training strategy tailored for multimodal MRI data. The same pre-trained model seamlessly adapts to any combination of available modalities, extracting rich representations that capture both intra- and inter-modal information. This allows fine-tuning on any subset of modalities without requiring architectural changes, while still benefiting from a model pre-trained on the full set of modalities. Extensive experiments show that the proposed pre-training strategy outperforms or remains competitive with baselines that require separate pre-training for each modality subset, while substantially surpassing training from scratch on several downstream tasks. Additionally, it can quickly and efficiently reconstruct missing modalities, highlighting its practical value. Code and trained models are available at: https://github.com/Lucas-rbnt/BM-MAE

Purpose: Magnetic resonance imaging (MRI) to visualize anatomical motion is becoming increasingly important when treating cancer patients with radiotherapy. Hybrid MRI-linear accelerator (MRI-linac) systems allow real-time motion management during irradiation. This paper presents a multi-institutional real-time MRI time series dataset from different MRI-linac vendors. The dataset is designed to support developing and evaluating real-time tumor localization (tracking) algorithms for MRI-guided radiotherapy within the TrackRAD2025 challenge (https://trackrad2025.grand-challenge.org/). Acquisition and validation methods: The dataset consists of sagittal 2D cine MRIs in 585 patients from six centers (3 Dutch, 1 German, 1 Australian, and 1 Chinese). Tumors in the thorax, abdomen, and pelvis acquired on two commercially available MRI-linacs (0.35 T and 1.5 T) were included. For 108 cases, irradiation targets or tracking surrogates were manually segmented on each temporal frame. The dataset was randomly split into a public training set of 527 cases (477 unlabeled and 50 labeled) and a private testing set of 58 cases (all labeled). Data Format and Usage Notes: The data is publicly available under the TrackRAD2025 collection: https://doi.org/10.57967/hf/4539. Both the images and segmentations for each patient are available in metadata format. Potential Applications: This novel clinical dataset will enable the development and evaluation of real-time tumor localization algorithms for MRI-guided radiotherapy. By enabling more accurate motion management and adaptive treatment strategies, this dataset has the potential to advance the field of radiotherapy significantly.

Functional magnetic resonance imaging (fMRI) is an indispensable tool in modern neuroscience, providing a non-invasive window into whole-brain dynamics at millimeter-scale spatial resolution. However, fMRI is constrained by issues such as high operation costs and immobility. With the rapid advancements in cross-modality synthesis and brain decoding, the use of deep neural networks has emerged as a promising solution for inferring whole-brain, high-resolution fMRI features directly from electroencephalography (EEG), a more widely accessible and portable neuroimaging modality. Nonetheless, the complex projection from neural activity to fMRI hemodynamic responses and the spatial ambiguity of EEG pose substantial challenges both in modeling and interpretability. Relatively few studies to date have developed approaches for EEG-fMRI translation, and although they have made significant strides, the inference of fMRI signals in a given study has been limited to a small set of brain areas and to a single condition (i.e., either resting-state or a specific task). The capability to predict fMRI signals in other brain areas, as well as to generalize across conditions, remain critical gaps in the field. To tackle these challenges, we introduce a novel and generalizable framework: NeuroBOLT, i.e., Neuro-to-BOLD Transformer, which leverages multi-dimensional representation learning from temporal, spatial, and spectral domains to translate raw EEG data to the corresponding fMRI activity signals across the brain. Our experiments demonstrate that NeuroBOLT effectively reconstructs unseen resting-state fMRI signals from primary sensory, high-level cognitive areas, and deep subcortical brain regions, achieving state-of-the-art accuracy with the potential to generalize across varying conditions and sites, which significantly advances the integration of these two modalities.

Segmenting stroke lesions in Magnetic Resonance Imaging (MRI) is challenging due to diverse clinical imaging domains, with existing models struggling to generalise across different MRI acquisition parameters and sequences. In this work, we propose two novel physics-constrained approaches using synthetic quantitative MRI (qMRI) images to enhance the robustness and generalisability of segmentation models. We trained a qMRI estimation model to predict qMRI maps from MPRAGE images, which were used to simulate diverse MRI sequences for segmentation training. A second approach built upon prior work in synthetic data for stroke lesion segmentation, generating qMRI maps from a dataset of tissue labels. The proposed approaches improved over the baseline nnUNet on a variety of out-of-distribution datasets, with the second approach outperforming the prior synthetic data method.

Deep-learning-based brain magnetic resonance imaging (MRI) reconstruction methods have the potential to accelerate the MRI acquisition process. Nevertheless, the scientific community lacks appropriate benchmarks to assess MRI reconstruction quality of high-resolution brain images, and evaluate how these proposed algorithms will behave in the presence of small, but expected data distribution shifts. The Multi-Coil Magnetic Resonance Image (MC-MRI) Reconstruction Challenge provides a benchmark that aims at addressing these issues, using a large dataset of high-resolution, three-dimensional, T1-weighted MRI scans. The challenge has two primary goals: 1) to compare different MRI reconstruction models on this dataset and 2) to assess the generalizability of these models to data acquired with a different number of receiver coils. In this paper, we describe the challenge experimental design, and summarize the results of a set of baseline and state of the art brain MRI reconstruction models. We provide relevant comparative information on the current MRI reconstruction state-of-the-art and highlight the challenges of obtaining generalizable models that are required prior to broader clinical adoption. The MC-MRI benchmark data, evaluation code and current challenge leaderboard are publicly available. They provide an objective performance assessment for future developments in the field of brain MRI reconstruction.

Multi-modality magnetic resonance imaging data with various sequences facilitate the early diagnosis, tumor segmentation, and disease staging in the management of nasopharyngeal carcinoma (NPC). The lack of publicly available, comprehensive datasets limits advancements in diagnosis, treatment planning, and the development of machine learning algorithms for NPC. Addressing this critical need, we introduce the first comprehensive NPC MRI dataset, encompassing MR axial imaging of 277 primary NPC patients. This dataset includes T1-weighted, T2-weighted, and contrast-enhanced T1-weighted sequences, totaling 831 scans. In addition to the corresponding clinical data, manually annotated and labeled segmentations by experienced radiologists offer high-quality data resources from untreated primary NPC.

Reconstruction of magnetic resonance imaging (MRI) data has been positively affected by deep learning. A key challenge remains: to improve generalisation to distribution shifts between the training and testing data. Most approaches aim to address this via inductive design or data augmentation. However, they can be affected by misleading data, e.g. random noise, and cases where the inference stage data do not match assumptions in the modelled shifts. In this work, by employing a conditional hyperparameter network, we eliminate the need of augmentation, yet maintain robust performance under various levels of Gaussian noise. We demonstrate that our model withstands various input noise levels while producing high-definition reconstructions during the test stage. Moreover, we present a hyperparameter sampling strategy that accelerates the convergence of training. Our proposed method achieves the highest accuracy and image quality in all settings compared to baseline methods.

We describe a Magnetic Resonance Imaging (MRI) dataset from individuals from the African nation of Nigeria. The dataset contains pseudonymized structural MRI (T1w, T2w, FLAIR) data of clinical quality. The dataset contains data from 36 images from healthy control subjects, 32 images from individuals diagnosed with age-related dementia and 20 from individuals with Parkinson's disease. There is currently a paucity of data from the African continent. Given the potential for Africa to contribute to the global neuroscience community, this first MRI dataset represents both an opportunity and benchmark for future studies to share data from the African continent.

Breast dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) plays an important role in the screening and prognosis assessment of high-risk breast cancer. The segmentation of cancerous regions is essential useful for the subsequent analysis of breast MRI. To alleviate the annotation effort to train the segmentation networks, we propose a weakly-supervised strategy using extreme points as annotations for breast cancer segmentation. Without using any bells and whistles, our strategy focuses on fully exploiting the learning capability of the routine training procedure, i.e., the train - fine-tune - retrain process. The network first utilizes the pseudo-masks generated using the extreme points to train itself, by minimizing a contrastive loss, which encourages the network to learn more representative features for cancerous voxels. Then the trained network fine-tunes itself by using a similarity-aware propagation learning (SimPLe) strategy, which leverages feature similarity between unlabeled and positive voxels to propagate labels. Finally the network retrains itself by employing the pseudo-masks generated using previous fine-tuned network. The proposed method is evaluated on our collected DCE-MRI dataset containing 206 patients with biopsy-proven breast cancers. Experimental results demonstrate our method effectively fine-tunes the network by using the SimPLe strategy, and achieves a mean Dice value of 81%.

Every day, the human brain processes an immense volume of visual information, relying on intricate neural mechanisms to perceive and interpret these stimuli. Recent breakthroughs in functional magnetic resonance imaging (fMRI) have enabled scientists to extract visual information from human brain activity patterns. In this study, we present an innovative method for decoding brain activity into meaningful images and captions, with a specific focus on brain captioning due to its enhanced flexibility as compared to brain decoding into images. Our approach takes advantage of cutting-edge image captioning models and incorporates a unique image reconstruction pipeline that utilizes latent diffusion models and depth estimation. We utilized the Natural Scenes Dataset, a comprehensive fMRI dataset from eight subjects who viewed images from the COCO dataset. We employed the Generative Image-to-text Transformer (GIT) as our backbone for captioning and propose a new image reconstruction pipeline based on latent diffusion models. The method involves training regularized linear regression models between brain activity and extracted features. Additionally, we incorporated depth maps from the ControlNet model to further guide the reconstruction process. We evaluate our methods using quantitative metrics for both generated captions and images. Our brain captioning approach outperforms existing methods, while our image reconstruction pipeline generates plausible images with improved spatial relationships. In conclusion, we demonstrate significant progress in brain decoding, showcasing the enormous potential of integrating vision and language to better understand human cognition. Our approach provides a flexible platform for future research, with potential applications in various fields, including neural art, style transfer, and portable devices.

Computed tomography and magnetic resonance imaging are two widely used clinical imaging modalities for non-invasive diagnosis. However, both of these modalities come with certain problems. CT uses harmful ionising radiation, and MRI suffers from slow acquisition speed. Both problems can be tackled by undersampling, such as sparse sampling. However, such undersampled data leads to lower resolution and introduces artefacts. Several techniques, including deep learning based methods, have been proposed to reconstruct such data. However, the undersampled reconstruction problem for these two modalities was always considered as two different problems and tackled separately by different research works. This paper proposes a unified solution for both sparse CT and undersampled radial MRI reconstruction, achieved by applying Fourier transform-based pre-processing on the radial MRI and then finally reconstructing both modalities using sinogram upsampling combined with filtered back-projection. The Primal-Dual network is a deep learning based method for reconstructing sparsely-sampled CT data. This paper introduces Primal-Dual UNet, which improves the Primal-Dual network in terms of accuracy and reconstruction speed. The proposed method resulted in an average SSIM of 0.932\textpm0.021 while performing sparse CT reconstruction for fan-beam geometry with a sparsity level of 16, achieving a statistically significant improvement over the previous model, which resulted in 0.919\textpm0.016. Furthermore, the proposed model resulted in 0.903\textpm0.019 and 0.957\textpm0.023 average SSIM while reconstructing undersampled brain and abdominal MRI data with an acceleration factor of 16, respectively - statistically significant improvements over the original model, which resulted in 0.867\textpm0.025 and 0.949\textpm0.025.

Reconstructing 3D visuals from functional Magnetic Resonance Imaging (fMRI) data, introduced as Recon3DMind in our conference work, is of significant interest to both cognitive neuroscience and computer vision. To advance this task, we present the fMRI-3D dataset, which includes data from 15 participants and showcases a total of 4768 3D objects. The dataset comprises two components: fMRI-Shape, previously introduced and accessible at https://huggingface.co/datasets/Fudan-fMRI/fMRI-Shape, and fMRI-Objaverse, proposed in this paper and available at https://huggingface.co/datasets/Fudan-fMRI/fMRI-Objaverse. fMRI-Objaverse includes data from 5 subjects, 4 of whom are also part of the Core set in fMRI-Shape, with each subject viewing 3142 3D objects across 117 categories, all accompanied by text captions. This significantly enhances the diversity and potential applications of the dataset. Additionally, we propose MinD-3D, a novel framework designed to decode 3D visual information from fMRI signals. The framework first extracts and aggregates features from fMRI data using a neuro-fusion encoder, then employs a feature-bridge diffusion model to generate visual features, and finally reconstructs the 3D object using a generative transformer decoder. We establish new benchmarks by designing metrics at both semantic and structural levels to evaluate model performance. Furthermore, we assess our model's effectiveness in an Out-of-Distribution setting and analyze the attribution of the extracted features and the visual ROIs in fMRI signals. Our experiments demonstrate that MinD-3D not only reconstructs 3D objects with high semantic and spatial accuracy but also deepens our understanding of how human brain processes 3D visual information. Project page at: https://jianxgao.github.io/MinD-3D.

Automatic identification of brain lesions from magnetic resonance imaging (MRI) scans of stroke survivors would be a useful aid in patient diagnosis and treatment planning. We propose a multi-modal multi-path convolutional neural network system for automating stroke lesion segmentation. Our system has nine end-to-end UNets that take as input 2-dimensional (2D) slices and examines all three planes with three different normalizations. Outputs from these nine total paths are concatenated into a 3D volume that is then passed to a 3D convolutional neural network to output a final lesion mask. We trained and tested our method on datasets from three sources: Medical College of Wisconsin (MCW), Kessler Foundation (KF), and the publicly available Anatomical Tracings of Lesions After Stroke (ATLAS) dataset. Cross-study validation results (with independent training and validation datasets) were obtained to compare with previous methods based on naive Bayes, random forests, and three recently published convolutional neural networks. Model performance was quantified in terms of the Dice coefficient. Training on the KF and MCW images and testing on the ATLAS images yielded a mean Dice coefficient of 0.54. This was reliably better than the next best previous model, UNet, at 0.47. Reversing the train and test datasets yields a mean Dice of 0.47 on KF and MCW images, whereas the next best UNet reaches 0.45. With all three datasets combined, the current system compared to previous methods also attained a reliably higher cross-validation accuracy. It also achieved high Dice values for many smaller lesions that existing methods have difficulty identifying. Overall, our system is a clear improvement over previous methods for automating stroke lesion segmentation, bringing us an important step closer to the inter-rater accuracy level of human experts.

Brain tumor detection in multiplane Magnetic Resonance Imaging (MRI) slices is a challenging task due to the various appearances and relationships in the structure of the multiplane images. In this paper, we propose a new You Only Look Once (YOLO)-based detection model that incorporates Pretrained Knowledge (PK), called PK-YOLO, to improve the performance for brain tumor detection in multiplane MRI slices. To our best knowledge, PK-YOLO is the first pretrained knowledge guided YOLO-based object detector. The main components of the new method are a pretrained pure lightweight convolutional neural network-based backbone via sparse masked modeling, a YOLO architecture with the pretrained backbone, and a regression loss function for improving small object detection. The pretrained backbone allows for feature transferability of object queries on individual plane MRI slices into the model encoders, and the learned domain knowledge base can improve in-domain detection. The improved loss function can further boost detection performance on small-size brain tumors in multiplanar two-dimensional MRI slices. Experimental results show that the proposed PK-YOLO achieves competitive performance on the multiplanar MRI brain tumor detection datasets compared to state-of-the-art YOLO-like and DETR-like object detectors. The code is available at https://github.com/mkang315/PK-YOLO.

Accurate 3D cardiac reconstruction from cine magnetic resonance imaging (cMRI) is crucial for improved cardiovascular disease diagnosis and understanding of the heart's motion. However, current cardiac MRI-based reconstruction technology used in clinical settings is 2D with limited through-plane resolution, resulting in low-quality reconstructed cardiac volumes. To better reconstruct 3D cardiac volumes from sparse 2D image stacks, we propose a morphology-guided diffusion model for 3D cardiac volume reconstruction, DMCVR, that synthesizes high-resolution 2D images and corresponding 3D reconstructed volumes. Our method outperforms previous approaches by conditioning the cardiac morphology on the generative model, eliminating the time-consuming iterative optimization process of the latent code, and improving generation quality. The learned latent spaces provide global semantics, local cardiac morphology and details of each 2D cMRI slice with highly interpretable value to reconstruct 3D cardiac shape. Our experiments show that DMCVR is highly effective in several aspects, such as 2D generation and 3D reconstruction performance. With DMCVR, we can produce high-resolution 3D cardiac MRI reconstructions, surpassing current techniques. Our proposed framework has great potential for improving the accuracy of cardiac disease diagnosis and treatment planning. Code can be accessed at https://github.com/hexiaoxiao-cs/DMCVR.

Deciphering visual content from functional Magnetic Resonance Imaging (fMRI) helps illuminate the human vision system. However, the scarcity of fMRI data and noise hamper brain decoding model performance. Previous approaches primarily employ subject-specific models, sensitive to training sample size. In this paper, we explore a straightforward but overlooked solution to address data scarcity. We propose shallow subject-specific adapters to map cross-subject fMRI data into unified representations. Subsequently, a shared deeper decoding model decodes cross-subject features into the target feature space. During training, we leverage both visual and textual supervision for multi-modal brain decoding. Our model integrates a high-level perception decoding pipeline and a pixel-wise reconstruction pipeline guided by high-level perceptions, simulating bottom-up and top-down processes in neuroscience. Empirical experiments demonstrate robust neural representation learning across subjects for both pipelines. Moreover, merging high-level and low-level information improves both low-level and high-level reconstruction metrics. Additionally, we successfully transfer learned general knowledge to new subjects by training new adapters with limited training data. Compared to previous state-of-the-art methods, notably pre-training-based methods (Mind-Vis and fMRI-PTE), our approach achieves comparable or superior results across diverse tasks, showing promise as an alternative method for cross-subject fMRI data pre-training. Our code and pre-trained weights will be publicly released at https://github.com/YulongBonjour/See_Through_Their_Minds.

The detailed images produced by Magnetic Resonance Imaging (MRI) provide life-critical information for the diagnosis and treatment of prostate cancer. To provide standardized acquisition, interpretation and usage of the complex MRI images, the PI-RADS v2 guideline was proposed. An automated segmentation following the guideline facilitates consistent and precise lesion detection, staging and treatment. The guideline recommends a division of the prostate into four zones, PZ (peripheral zone), TZ (transition zone), DPU (distal prostatic urethra) and AFS (anterior fibromuscular stroma). Not every zone shares a boundary with the others and is present in every slice. Further, the representations captured by a single model might not suffice for all zones. This motivated us to design a dual-branch convolutional neural network (CNN), where each branch captures the representations of the connected zones separately. Further, the representations from different branches act complementary to each other at the second stage of training, where they are fine-tuned through an unsupervised loss. The loss penalises the difference in predictions from the two branches for the same class. We also incorporate multi-task learning in our framework to further improve the segmentation accuracy. The proposed approach improves the segmentation accuracy of the baseline (mean absolute symmetric distance) by 7.56%, 11.00%, 58.43% and 19.67% for PZ, TZ, DPU and AFS zones respectively.

Autism spectrum disorder (ASD) is a prevalent psychiatric condition characterized by atypical cognitive, emotional, and social patterns. Timely and accurate diagnosis is crucial for effective interventions and improved outcomes in individuals with ASD. In this study, we propose a novel Multi-Atlas Enhanced Transformer framework, METAFormer, ASD classification. Our framework utilizes resting-state functional magnetic resonance imaging data from the ABIDE I dataset, comprising 406 ASD and 476 typical control (TC) subjects. METAFormer employs a multi-atlas approach, where flattened connectivity matrices from the AAL, CC200, and DOS160 atlases serve as input to the transformer encoder. Notably, we demonstrate that self-supervised pretraining, involving the reconstruction of masked values from the input, significantly enhances classification performance without the need for additional or separate training data. Through stratified cross-validation, we evaluate the proposed framework and show that it surpasses state-of-the-art performance on the ABIDE I dataset, with an average accuracy of 83.7% and an AUC-score of 0.832. The code for our framework is available at https://github.com/Lugges991/METAFormer

The removal of non-brain signal from magnetic resonance imaging (MRI) data, known as skull-stripping, is an integral component of many neuroimage analysis streams. Despite their abundance, popular classical skull-stripping methods are usually tailored to images with specific acquisition properties, namely near-isotropic resolution and T1-weighted (T1w) MRI contrast, which are prevalent in research settings. As a result, existing tools tend to adapt poorly to other image types, such as stacks of thick slices acquired with fast spin-echo (FSE) MRI that are common in the clinic. While learning-based approaches for brain extraction have gained traction in recent years, these methods face a similar burden, as they are only effective for image types seen during the training procedure. To achieve robust skull-stripping across a landscape of imaging protocols, we introduce SynthStrip, a rapid, learning-based brain-extraction tool. By leveraging anatomical segmentations to generate an entirely synthetic training dataset with anatomies, intensity distributions, and artifacts that far exceed the realistic range of medical images, SynthStrip learns to successfully generalize to a variety of real acquired brain images, removing the need for training data with target contrasts. We demonstrate the efficacy of SynthStrip for a diverse set of image acquisitions and resolutions across subject populations, ranging from newborn to adult. We show substantial improvements in accuracy over popular skull-stripping baselines -- all with a single trained model. Our method and labeled evaluation data are available at https://w3id.org/synthstrip.

We present a multilinear statistical model of the human tongue that captures anatomical and tongue pose related shape variations separately. The model is derived from 3D magnetic resonance imaging data of 11 speakers sustaining speech related vocal tract configurations. The extraction is performed by using a minimally supervised method that uses as basis an image segmentation approach and a template fitting technique. Furthermore, it uses image denoising to deal with possibly corrupt data, palate surface information reconstruction to handle palatal tongue contacts, and a bootstrap strategy to refine the obtained shapes. Our evaluation concludes that limiting the degrees of freedom for the anatomical and speech related variations to 5 and 4, respectively, produces a model that can reliably register unknown data while avoiding overfitting effects. Furthermore, we show that it can be used to generate a plausible tongue animation by tracking sparse motion capture data.

Brain signal visualization has emerged as an active research area, serving as a critical interface between the human visual system and computer vision models. Although diffusion models have shown promise in analyzing functional magnetic resonance imaging (fMRI) data, including reconstructing high-quality images consistent with original visual stimuli, their accuracy in extracting semantic and silhouette information from brain signals remains limited. In this regard, we propose a novel approach, referred to as Controllable Mind Visual Diffusion Model (CMVDM). CMVDM extracts semantic and silhouette information from fMRI data using attribute alignment and assistant networks. Additionally, a residual block is incorporated to capture information beyond semantic and silhouette features. We then leverage a control model to fully exploit the extracted information for image synthesis, resulting in generated images that closely resemble the visual stimuli in terms of semantics and silhouette. Through extensive experimentation, we demonstrate that CMVDM outperforms existing state-of-the-art methods both qualitatively and quantitatively.

This paper presents a large publicly available multi-center lumbar spine magnetic resonance imaging (MRI) dataset with reference segmentations of vertebrae, intervertebral discs (IVDs), and spinal canal. The dataset includes 447 sagittal T1 and T2 MRI series from 218 patients with a history of low back pain. It was collected from four different hospitals and was divided into a training (179 patients) and validation (39 patients) set. An iterative data annotation approach was used by training a segmentation algorithm on a small part of the dataset, enabling semi-automatic segmentation of the remaining images. The algorithm provided an initial segmentation, which was subsequently reviewed, manually corrected, and added to the training data. We provide reference performance values for this baseline algorithm and nnU-Net, which performed comparably. We set up a continuous segmentation challenge to allow for a fair comparison of different segmentation algorithms. This study may encourage wider collaboration in the field of spine segmentation, and improve the diagnostic value of lumbar spine MRI.

Medical imaging is critical for diagnostics, but clinical adoption of advanced AI-driven imaging faces challenges due to patient variability, image artifacts, and limited model generalization. While deep learning has transformed image analysis, 3D medical imaging still suffers from data scarcity and inconsistencies due to acquisition protocols, scanner differences, and patient motion. Traditional augmentation uses a single pipeline for all transformations, disregarding the unique traits of each augmentation and struggling with large data volumes. To address these challenges, we propose a Multi-encoder Augmentation-Aware Learning (MEAL) framework that leverages four distinct augmentation variants processed through dedicated encoders. Three fusion strategies such as concatenation (CC), fusion layer (FL), and adaptive controller block (BD) are integrated to build multi-encoder models that combine augmentation-specific features before decoding. MEAL-BD uniquely preserves augmentation-aware representations, enabling robust, protocol-invariant feature learning. As demonstrated in a Computed Tomography (CT)-to-T1-weighted Magnetic Resonance Imaging (MRI) translation study, MEAL-BD consistently achieved the best performance on both unseen- and predefined-test data. On both geometric transformations (like rotations and flips) and non-augmented inputs, MEAL-BD outperformed other competing methods, achieving higher mean peak signal-to-noise ratio (PSNR) and structural similarity index measure (SSIM) scores. These results establish MEAL as a reliable framework for preserving structural fidelity and generalizing across clinically relevant variability. By reframing augmentation as a source of diverse, generalizable features, MEAL supports robust, protocol-invariant learning, advancing clinically reliable medical imaging solutions.

A major challenge of the long measurement times in magnetic resonance imaging (MRI), an important medical imaging technology, is that patients may move during data acquisition. This leads to severe motion artifacts in the reconstructed images and volumes. In this paper, we propose a deep learning-based test-time-training method for accurate motion estimation. The key idea is that a neural network trained for motion-free reconstruction has a small loss if there is no motion, thus optimizing over motion parameters passed through the reconstruction network enables accurate estimation of motion. The estimated motion parameters enable to correct for the motion and to reconstruct accurate motion-corrected images. Our method uses 2D reconstruction networks to estimate rigid motion in 3D, and constitutes the first deep learning based method for 3D rigid motion estimation towards 3D-motion-corrected MRI. We show that our method can provably reconstruct motion parameters for a simple signal and neural network model. We demonstrate the effectiveness of our method for both retrospectively simulated motion and prospectively collected real motion-corrupted data.

Alzheimer's Disease (AD) is a progressive neurodegenerative disorder that primarily affects the aging population by impairing cognitive and motor functions. Early detection of AD through accessible methodologies like magnetic resonance imaging (MRI) is vital for developing effective interventions to halt or slow the disease's progression. This study aims to perform a comprehensive analysis of machine learning techniques for selecting MRI-based biomarkers and classifying individuals into healthy controls (HC) and unstable controls (uHC) who later show mild cognitive impairment within five years. The research utilizes MRI data from the Alzheimer's Disease Neuroinformatics Initiative (ADNI) and the Open Access Series of Imaging Studies 3 (OASIS-3), focusing on both HC and uHC participants. The study addresses the challenges of imbalanced data by testing classification methods on balanced and unbalanced datasets, and harmonizes data using polynomial regression to mitigate nuisance variables like age, gender, and intracranial volume. Results indicate that Gaussian Naive Bayes and RusBoost classifiers shows an optimal performance, achieving accuracies of up to 76.46% and 72.48% respectively on the ADNI dataset. For the OASIS-3 dataset, Kernel Naive Bayes and RusBoost yield accuracies ranging from 64.66% to 75.71%, improving further in age-matched datasets. Brain regions like the entorhinal cortex, hippocampus, lateral ventricle, and lateral orbitofrontal cortex are identified as significantly impacted during early cognitive decline. Despite limitations such as small sample sizes, the study's harmonization approach enhances the robustness of biomarker selection, suggesting the potential of this semi-automatic machine learning pipeline for early AD detection using MRI.

Hyperthermia (HT) in combination with radio- and/or chemotherapy has become an accepted cancer treatment for distinct solid tumour entities. In HT, tumour tissue is exogenously heated to temperatures between 39 and 43 ^circC for 60 minutes. Temperature monitoring can be performed non-invasively using dynamic magnetic resonance imaging (MRI). However, the slow nature of MRI leads to motion artefacts in the images due to the movements of patients during image acquisition. By discarding parts of the data, the speed of the acquisition can be increased - known as undersampling. However, due to the invalidation of the Nyquist criterion, the acquired images might be blurry and can also produce aliasing artefacts. The aim of this work was, therefore, to reconstruct highly undersampled MR thermometry acquisitions with better resolution and with fewer artefacts compared to conventional methods. The use of deep learning in the medical field has emerged in recent times, and various studies have shown that deep learning has the potential to solve inverse problems such as MR image reconstruction. However, most of the published work only focuses on the magnitude images, while the phase images are ignored, which are fundamental requirements for MR thermometry. This work, for the first time, presents deep learning-based solutions for reconstructing undersampled MR thermometry data. Two different deep learning models have been employed here, the Fourier Primal-Dual network and the Fourier Primal-Dual UNet, to reconstruct highly undersampled complex images of MR thermometry. The method reduced the temperature difference between the undersampled MRIs and the fully sampled MRIs from 1.3 ^circC to 0.6 ^circC in full volume and 0.49 ^circC to 0.06 ^circC in the tumour region for an acceleration factor of 10.

Clinical routine and retrospective cohorts commonly include multi-parametric Magnetic Resonance Imaging; however, they are mostly acquired in different anisotropic 2D views due to signal-to-noise-ratio and scan-time constraints. Thus acquired views suffer from poor out-of-plane resolution and affect downstream volumetric image analysis that typically requires isotropic 3D scans. Combining different views of multi-contrast scans into high-resolution isotropic 3D scans is challenging due to the lack of a large training cohort, which calls for a subject-specific framework. This work proposes a novel solution to this problem leveraging Implicit Neural Representations (INR). Our proposed INR jointly learns two different contrasts of complementary views in a continuous spatial function and benefits from exchanging anatomical information between them. Trained within minutes on a single commodity GPU, our model provides realistic super-resolution across different pairs of contrasts in our experiments with three datasets. Using Mutual Information (MI) as a metric, we find that our model converges to an optimum MI amongst sequences, achieving anatomically faithful reconstruction. Code is available at: https://github.com/jqmcginnis/multi_contrast_inr/

Although deep learning (DL) has received much attention in accelerated magnetic resonance imaging (MRI), recent studies show that tiny input perturbations may lead to instabilities of DL-based MRI reconstruction models. However, the approaches of robustifying these models are underdeveloped. Compared to image classification, it could be much more challenging to achieve a robust MRI image reconstruction network considering its regression-based learning objective, limited amount of training data, and lack of efficient robustness metrics. To circumvent the above limitations, our work revisits the problem of DL-based image reconstruction through the lens of robust machine learning. We find a new instability source of MRI image reconstruction, i.e., the lack of reconstruction robustness against spatial transformations of an input, e.g., rotation and cutout. Inspired by this new robustness metric, we develop a robustness-aware image reconstruction method that can defend against both pixel-wise adversarial perturbations as well as spatial transformations. Extensive experiments are also conducted to demonstrate the effectiveness of our proposed approaches.

A brain tumour is a mass or cluster of abnormal cells in the brain, which has the possibility of becoming life-threatening because of its ability to invade neighbouring tissues and also form metastases. An accurate diagnosis is essential for successful treatment planning and magnetic resonance imaging is the principal imaging modality for diagnostic of brain tumours and their extent. Deep Learning methods in computer vision applications have shown significant improvement in recent years, most of which can be credited to the fact that a sizeable amount of data is available to train models on, and the improvements in the model architectures yielding better approximations in a supervised setting. Classifying tumours using such deep learning methods has made significant progress with the availability of open datasets with reliable annotations. Typically those methods are either 3D models, which use 3D volumetric MRIs or even 2D models considering each slice separately. However, by treating the slice spatial dimension separately, spatiotemporal models can be employed as spatiospatial models for this task. These models have the capabilities of learning specific spatial and temporal relationship, while reducing computational costs. This paper uses two spatiotemporal models, ResNet (2+1)D and ResNet Mixed Convolution, to classify different types of brain tumours. It was observed that both these models performed superior to the pure 3D convolutional model, ResNet18. Furthermore, it was also observed that pre-training the models on a different, even unrelated dataset before training them for the task of tumour classification improves the performance. Finally, Pre-trained ResNet Mixed Convolution was observed to be the best model in these experiments, achieving a macro F1-score of 0.93 and a test accuracy of 96.98\%, while at the same time being the model with the least computational cost.

To improve patient survival and treatment outcomes, early diagnosis of brain tumors is an essential task. It is a difficult task to evaluate the magnetic resonance imaging (MRI) images manually. Thus, there is a need for digital methods for tumor diagnosis with better accuracy. However, it is still a very challenging task in assessing their shape, volume, boundaries, tumor detection, size, segmentation, and classification. In this proposed work, we propose a hybrid ensemble method using Random Forest (RF), K-Nearest Neighbour, and Decision Tree (DT) (KNN-RF-DT) based on Majority Voting Method. It aims to calculate the area of the tumor region and classify brain tumors as benign and malignant. In the beginning, segmentation is done by using Otsu's Threshold method. Feature Extraction is done by using Stationary Wavelet Transform (SWT), Principle Component Analysis (PCA), and Gray Level Co-occurrence Matrix (GLCM), which gives thirteen features for classification. The classification is done by hybrid ensemble classifier (KNN-RF-DT) based on the Majority Voting method. Overall it aimed at improving the performance by traditional classifiers instead of going to deep learning. Traditional classifiers have an advantage over deep learning algorithms because they require small datasets for training and have low computational time complexity, low cost to the users, and can be easily adopted by less skilled people. Overall, our proposed method is tested upon dataset of 2556 images, which are used in 85:15 for training and testing respectively and gives good accuracy of 97.305%.

A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark. The code is made public at https://github.com/krishnabits001/domain_specific_cl.

Deep neural networks trained on Functional Connectivity (FC) networks extracted from functional Magnetic Resonance Imaging (fMRI) data have gained popularity due to the increasing availability of data and advances in model architectures, including Graph Neural Network (GNN). Recent research on the application of GNN to FC suggests that exploiting the time-varying properties of the FC could significantly improve the accuracy and interpretability of the model prediction. However, the high cost of acquiring high-quality fMRI data and corresponding phenotypic labels poses a hurdle to their application in real-world settings, such that a model na\"ively trained in a supervised fashion can suffer from insufficient performance or a lack of generalization on a small number of data. In addition, most Self-Supervised Learning (SSL) approaches for GNNs to date adopt a contrastive strategy, which tends to lose appropriate semantic information when the graph structure is perturbed or does not leverage both spatial and temporal information simultaneously. In light of these challenges, we propose a generative SSL approach that is tailored to effectively harness spatio-temporal information within dynamic FC. Our empirical results, experimented with large-scale (>50,000) fMRI datasets, demonstrate that our approach learns valuable representations and enables the construction of accurate and robust models when fine-tuned for downstream tasks.

Detecting breast cancer early is of the utmost importance to effectively treat the millions of women afflicted by breast cancer worldwide every year. Although mammography is the primary imaging modality for screening breast cancer, there is an increasing interest in adding magnetic resonance imaging (MRI) to screening programmes, particularly for women at high risk. Recent guidelines by the European Society of Breast Imaging (EUSOBI) recommended breast MRI as a supplemental screening tool for women with dense breast tissue. However, acquiring and reading MRI scans requires significantly more time from expert radiologists. This highlights the need to develop new automated methods to detect cancer accurately using MRI and Artificial Intelligence (AI), which have the potential to support radiologists in breast MRI interpretation and classification and help detect cancer earlier. For this reason, the ODELIA consortium has made this multi-centre dataset publicly available to assist in developing AI tools for the detection of breast cancer on MRI.

Segment Anything Model (SAM) has gained significant attention because of its ability to segment a variety of objects in images given a prompt. The recently developed SAM 2 has extended this ability to video inputs. This opens an opportunity to apply SAM to 3D images, one of the fundamental tasks in the medical imaging field. In this paper, we provide an extensive evaluation of SAM 2's ability to segment both 2D and 3D medical images. We collect 18 medical imaging datasets, including common 3D modalities such as computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET) as well as 2D modalities such as X-ray and ultrasound. We consider two evaluation pipelines of SAM 2: (1) multi-frame 3D segmentation, where prompts are provided to one or multiple slice(s) selected from the volume, and (2) single-frame 2D segmentation, where prompts are provided to each slice. The former is only applicable to 3D modalities, while the latter applies to both 2D and 3D modalities. We learn that SAM 2 exhibits similar performance as SAM under single-frame 2D segmentation, and has variable performance under multi-frame 3D segmentation depending on the choices of slices to annotate, the direction of the propagation, the predictions utilized during the propagation, etc.

Neural decoding, the process of understanding how brain activity corresponds to different stimuli, has been a primary objective in cognitive sciences. Over the past three decades, advancements in functional Magnetic Resonance Imaging and machine learning have greatly improved our ability to map visual stimuli to brain activity, especially in the visual cortex. Concurrently, research has expanded into decoding more complex processes like language and memory across the whole brain, utilizing techniques to handle greater variability and improve signal accuracy. We argue that "seeing" involves more than just mapping visual stimuli onto the visual cortex; it engages the entire brain, as various emotions and cognitive states can emerge from observing different scenes. In this paper, we develop algorithms to enhance our understanding of visual processes by incorporating whole-brain activation maps while individuals are exposed to visual stimuli. We utilize large-scale fMRI encoders and Image generative models pre-trained on large public datasets, which are then fine-tuned through Image-fMRI contrastive learning. Our models hence can decode visual experience across the entire cerebral cortex, surpassing the traditional confines of the visual cortex. We first compare our method with state-of-the-art approaches to decoding visual processing and show improved predictive semantic accuracy by 43%. A network ablation analysis suggests that beyond the visual cortex, the default mode network contributes most to decoding stimuli, in line with the proposed role of this network in sense-making and semantic processing. Additionally, we implemented zero-shot imagination decoding on an extra validation dataset, achieving a p-value of 0.0206 for mapping the reconstructed images and ground-truth text stimuli, which substantiates the model's capability to capture semantic meanings across various scenarios.

Early diagnosis of mild cognitive impairment (MCI) and subjective cognitive decline (SCD) utilizing multi-modal magnetic resonance imaging (MRI) is a pivotal area of research. While various regional and connectivity features from functional MRI (fMRI) and diffusion tensor imaging (DTI) have been employed to develop diagnosis models, most studies integrate these features without adequately addressing their alignment and interactions. This limits the potential to fully exploit the synergistic contributions of combined features and modalities. To solve this gap, our study introduces a novel Hierarchical Alignments and Hierarchical Interactions (HA-HI) method for MCI and SCD classification, leveraging the combined strengths of fMRI and DTI. HA-HI efficiently learns significant MCI- or SCD- related regional and connectivity features by aligning various feature types and hierarchically maximizing their interactions. Furthermore, to enhance the interpretability of our approach, we have developed the Synergistic Activation Map (SAM) technique, revealing the critical brain regions and connections that are indicative of MCI/SCD. Comprehensive evaluations on the ADNI dataset and our self-collected data demonstrate that HA-HI outperforms other existing methods in diagnosing MCI and SCD, making it a potentially vital and interpretable tool for early detection. The implementation of this method is publicly accessible at https://github.com/ICI-BCI/Dual-MRI-HA-HI.git.

The increasing prevalence of lumbar spinal canal stenosis has resulted in a surge of MRI (Magnetic Resonance Imaging), leading to labor-intensive interpretation and significant inter-reader variability, even among expert radiologists. This paper introduces a novel and efficient deep-learning framework that fully automates the grading of lumbar spinal canal stenosis. We demonstrate state-of-the-art performance in grading spinal canal stenosis on a dataset of 1,975 unique studies, each containing three distinct types of 3D cross-sectional spine images: Axial T2, Sagittal T1, and Sagittal T2/STIR. Employing a distinctive training strategy, our proposed multistage approach effectively integrates sagittal and axial images. This strategy employs a multi-view model with a sequence-based architecture, optimizing feature extraction and cross-view alignment to achieve an AUROC (Area Under the Receiver Operating Characteristic Curve) of 0.971 in spinal canal stenosis grading surpassing other state-of-the-art methods.

Pulmonary Hypertension (PH) is a severe disease characterized by an elevated pulmonary artery pressure. The gold standard for PH diagnosis is measurement of mean Pulmonary Artery Pressure (mPAP) during an invasive Right Heart Catheterization. In this paper, we investigate noninvasive approach to PH detection utilizing Magnetic Resonance Imaging, Computer Models and Machine Learning. We show using the ablation study, that physics-informed feature engineering based on models of blood circulation increases the performance of Gradient Boosting Decision Trees-based algorithms for classification of PH and regression of values of mPAP. We compare results of regression (with thresholding of estimated mPAP) and classification and demonstrate that metrics achieved in both experiments are comparable. The predicted mPAP values are more informative to the physicians than the probability of PH returned by classification models. They provide the intuitive explanation of the outcome of the machine learning model (clinicians are accustomed to the mPAP metric, contrary to the PH probability).

The parcellation of Cranial Nerves (CNs) serves as a crucial quantitative methodology for evaluating the morphological characteristics and anatomical pathways of specific CNs. Multi-modal CNs parcellation networks have achieved promising segmentation performance, which combine structural Magnetic Resonance Imaging (MRI) and diffusion MRI. However, insufficient exploration of diffusion MRI information has led to low performance of existing multi-modal fusion. In this work, we propose a tractography-guided Dual-label Collaborative Learning Network (DCLNet) for multi-modal CNs parcellation. The key contribution of our DCLNet is the introduction of coarse labels of CNs obtained from fiber tractography through CN atlas, and collaborative learning with precise labels annotated by experts. Meanwhile, we introduce a Modality-adaptive Encoder Module (MEM) to achieve soft information swapping between structural MRI and diffusion MRI. Extensive experiments conducted on the publicly available Human Connectome Project (HCP) dataset demonstrate performance improvements compared to single-label network. This systematic validation underscores the effectiveness of dual-label strategies in addressing inherent ambiguities in CNs parcellation tasks.

Alzheimer's disease (AD) is a common neurodegenerative disease among the elderly. Early prediction and timely intervention of its prodromal stage, mild cognitive impairment (MCI), can decrease the risk of advancing to AD. Combining information from various modalities can significantly improve predictive accuracy. However, challenges such as missing data and heterogeneity across modalities complicate multimodal learning methods as adding more modalities can worsen these issues. Current multimodal fusion techniques often fail to adapt to the complexity of medical data, hindering the ability to identify relationships between modalities. To address these challenges, we propose an innovative multimodal approach for predicting MCI conversion, focusing specifically on the issues of missing positron emission tomography (PET) data and integrating diverse medical information. The proposed incomplete triple-modal MCI conversion prediction network is tailored for this purpose. Through the missing modal generation module, we synthesize the missing PET data from the magnetic resonance imaging and extract features using specifically designed encoders. We also develop a channel aggregation module and a triple-modal co-attention fusion module to reduce feature redundancy and achieve effective multimodal data fusion. Furthermore, we design a loss function to handle missing modality issues and align cross-modal features. These components collectively harness multimodal data to boost network performance. Experimental results on the ADNI1 and ADNI2 datasets show that our method significantly surpasses existing unimodal and other multimodal models. Our code is available at https://github.com/justinhxy/ITFC.

This manuscript describes the first challenge on Federated Learning, namely the Federated Tumor Segmentation (FeTS) challenge 2021. International challenges have become the standard for validation of biomedical image analysis methods. However, the actual performance of participating (even the winning) algorithms on "real-world" clinical data often remains unclear, as the data included in challenges are usually acquired in very controlled settings at few institutions. The seemingly obvious solution of just collecting increasingly more data from more institutions in such challenges does not scale well due to privacy and ownership hurdles. Towards alleviating these concerns, we are proposing the FeTS challenge 2021 to cater towards both the development and the evaluation of models for the segmentation of intrinsically heterogeneous (in appearance, shape, and histology) brain tumors, namely gliomas. Specifically, the FeTS 2021 challenge uses clinically acquired, multi-institutional magnetic resonance imaging (MRI) scans from the BraTS 2020 challenge, as well as from various remote independent institutions included in the collaborative network of a real-world federation (https://www.fets.ai/). The goals of the FeTS challenge are directly represented by the two included tasks: 1) the identification of the optimal weight aggregation approach towards the training of a consensus model that has gained knowledge via federated learning from multiple geographically distinct institutions, while their data are always retained within each institution, and 2) the federated evaluation of the generalizability of brain tumor segmentation models "in the wild", i.e. on data from institutional distributions that were not part of the training datasets.

Generative adversarial networks (GANs) have shown promise for various problems including anomaly detection. When anomaly detection is performed using GAN models that learn only the features of normal data samples, data that are not similar to normal data are detected as abnormal samples. The present approach is developed by employing a dual-encoder in a bidirectional GAN architecture that is trained simultaneously with a generator and a discriminator network. Through the learning mechanism, the proposed method aims to reduce the problem of bad cycle consistency, in which a bidirectional GAN might not be able to reproduce samples with a large difference between normal and abnormal samples. We assume that bad cycle consistency occurs when the method does not preserve enough information of the sample data. We show that our proposed method performs well in capturing the distribution of normal samples, thereby improving anomaly detection on GAN-based models. Experiments are reported in which our method is applied to publicly available datasets, including application to a brain magnetic resonance imaging anomaly detection system.

The state-of-the-art models for medical image segmentation are variants of U-Net and fully convolutional networks (FCN). Despite their success, these models have two limitations: (1) their optimal depth is apriori unknown, requiring extensive architecture search or inefficient ensemble of models of varying depths; and (2) their skip connections impose an unnecessarily restrictive fusion scheme, forcing aggregation only at the same-scale feature maps of the encoder and decoder sub-networks. To overcome these two limitations, we propose UNet++, a new neural architecture for semantic and instance segmentation, by (1) alleviating the unknown network depth with an efficient ensemble of U-Nets of varying depths, which partially share an encoder and co-learn simultaneously using deep supervision; (2) redesigning skip connections to aggregate features of varying semantic scales at the decoder sub-networks, leading to a highly flexible feature fusion scheme; and (3) devising a pruning scheme to accelerate the inference speed of UNet++. We have evaluated UNet++ using six different medical image segmentation datasets, covering multiple imaging modalities such as computed tomography (CT), magnetic resonance imaging (MRI), and electron microscopy (EM), and demonstrating that (1) UNet++ consistently outperforms the baseline models for the task of semantic segmentation across different datasets and backbone architectures; (2) UNet++ enhances segmentation quality of varying-size objects -- an improvement over the fixed-depth U-Net; (3) Mask RCNN++ (Mask R-CNN with UNet++ design) outperforms the original Mask R-CNN for the task of instance segmentation; and (4) pruned UNet++ models achieve significant speedup while showing only modest performance degradation. Our implementation and pre-trained models are available at https://github.com/MrGiovanni/UNetPlusPlus.

Although new vision foundation models such as Segment Anything Model 2 (SAM2) have significantly enhanced zero-shot image segmentation capabilities, reliance on human-provided prompts poses significant challenges in adapting SAM2 to medical image segmentation tasks. Moreover, SAM2's performance in medical image segmentation was limited by the domain shift issue, since it was originally trained on natural images and videos. To address these challenges, we proposed SAM2 with support-set guided prompting (SAM2-SGP), a framework that eliminated the need for manual prompts. The proposed model leveraged the memory mechanism of SAM2 to generate pseudo-masks using image-mask pairs from a support set via a Pseudo-mask Generation (PMG) module. We further introduced a novel Pseudo-mask Attention (PMA) module, which used these pseudo-masks to automatically generate bounding boxes and enhance localized feature extraction by guiding attention to relevant areas. Furthermore, a low-rank adaptation (LoRA) strategy was adopted to mitigate the domain shift issue. The proposed framework was evaluated on both 2D and 3D datasets across multiple medical imaging modalities, including fundus photography, X-ray, computed tomography (CT), magnetic resonance imaging (MRI), positron emission tomography (PET), and ultrasound. The results demonstrated a significant performance improvement over state-of-the-art models, such as nnUNet and SwinUNet, as well as foundation models, such as SAM2 and MedSAM2, underscoring the effectiveness of the proposed approach. Our code is publicly available at https://github.com/astlian9/SAM_Support.

Accurate prostate cancer diagnosis remains challenging. Even when using MRI, radiologists exhibit low specificity and significant inter-observer variability, leading to potential delays or inaccuracies in identifying clinically significant cancers. This leads to numerous unnecessary biopsies and risks of missing clinically significant cancers. Here we present prostate vision contrastive network (ProViCNet), prostate organ-specific vision foundation models for Magnetic Resonance Imaging (MRI) and Trans-Rectal Ultrasound imaging (TRUS) for comprehensive cancer detection. ProViCNet was trained and validated using 4,401 patients across six institutions, as a prostate cancer detection model on radiology images relying on patch-level contrastive learning guided by biopsy confirmed radiologist annotations. ProViCNet demonstrated consistent performance across multiple internal and external validation cohorts with area under the receiver operating curve values ranging from 0.875 to 0.966, significantly outperforming radiologists in the reader study (0.907 versus 0.805, p<0.001) for mpMRI, while achieving 0.670 to 0.740 for TRUS. We also integrated ProViCNet with standard PSA to develop a virtual screening test, and we showed that we can maintain the high sensitivity for detecting clinically significant cancers while more than doubling specificity from 15% to 38% (p<0.001), thereby substantially reducing unnecessary biopsies. These findings highlight that ProViCNet's potential for enhancing prostate cancer diagnosis accuracy and reduce unnecessary biopsies, thereby optimizing diagnostic pathways.

The process of reconstructing experiences from human brain activity offers a unique lens into how the brain interprets and represents the world. In this paper, we introduce a method for reconstructing music from brain activity, captured using functional magnetic resonance imaging (fMRI). Our approach uses either music retrieval or the MusicLM music generation model conditioned on embeddings derived from fMRI data. The generated music resembles the musical stimuli that human subjects experienced, with respect to semantic properties like genre, instrumentation, and mood. We investigate the relationship between different components of MusicLM and brain activity through a voxel-wise encoding modeling analysis. Furthermore, we discuss which brain regions represent information derived from purely textual descriptions of music stimuli. We provide supplementary material including examples of the reconstructed music at https://google-research.github.io/seanet/brain2music

Attention Deficit Hyperactive Disorder (ADHD) is a common behavioral problem affecting children. In this work, we investigate the automatic classification of ADHD subjects using the resting state Functional Magnetic Resonance Imaging (fMRI) sequences of the brain. We show that the brain can be modeled as a functional network, and certain properties of the networks differ in ADHD subjects from control subjects. We compute the pairwise correlation of brain voxels' activity over the time frame of the experimental protocol which helps to model the function of a brain as a network. Different network features are computed for each of the voxels constructing the network. The concatenation of the network features of all the voxels in a brain serves as the feature vector. Feature vectors from a set of subjects are then used to train a PCA-LDA (principal component analysis-linear discriminant analysis) based classifier. We hypothesized that ADHD-related differences lie in some specific regions of the brain and using features only from those regions is sufficient to discriminate ADHD and control subjects. We propose a method to create a brain mask that includes the useful regions only and demonstrate that using the feature from the masked regions improves classification accuracy on the test data set. We train our classifier with 776 subjects and test on 171 subjects provided by The Neuro Bureau for the ADHD-200 challenge. We demonstrate the utility of graph-motif features, specifically the maps that represent the frequency of participation of voxels in network cycles of length 3. The best classification performance (69.59%) is achieved using 3-cycle map features with masking. Our proposed approach holds promise in being able to diagnose and understand the disorder.

Medical images often contain artificial markers added by doctors, which can negatively affect the accuracy of AI-based diagnosis. To address this issue and recover the missing visual contents, inpainting techniques are highly needed. However, existing inpainting methods require manual mask input, limiting their application scenarios. In this paper, we introduce a novel blind inpainting method that automatically completes visual contents without specifying masks for target areas in an image. Our proposed model includes a mask-free reconstruction network and an object-aware discriminator. The reconstruction network consists of two branches that predict the corrupted regions with artificial markers and simultaneously recover the missing visual contents. The object-aware discriminator relies on the powerful recognition capabilities of the dense object detector to ensure that the markers of reconstructed images cannot be detected in any local regions. As a result, the reconstructed image can be close to the clean one as much as possible. Our proposed method is evaluated on different medical image datasets, covering multiple imaging modalities such as ultrasound (US), magnetic resonance imaging (MRI), and electron microscopy (EM), demonstrating that our method is effective and robust against various unknown missing region patterns.

In this paper, we introduce Recon3DMind, an innovative task aimed at reconstructing 3D visuals from Functional Magnetic Resonance Imaging (fMRI) signals, marking a significant advancement in the fields of cognitive neuroscience and computer vision. To support this pioneering task, we present the fMRI-Shape dataset, which includes data from 14 participants and features 360-degree videos of 3D objects to enable comprehensive fMRI signal capture across various settings, thereby laying a foundation for future research. Furthermore, we propose MinD-3D, a novel and effective three-stage framework specifically designed to decode the brain's 3D visual information from fMRI signals, demonstrating the feasibility of this challenging task. The framework begins by extracting and aggregating features from fMRI frames through a neuro-fusion encoder, subsequently employs a feature bridge diffusion model to generate visual features, and ultimately recovers the 3D object via a generative transformer decoder. We assess the performance of MinD-3D using a suite of semantic and structural metrics and analyze the correlation between the features extracted by our model and the visual regions of interest (ROIs) in fMRI signals. Our findings indicate that MinD-3D not only reconstructs 3D objects with high semantic relevance and spatial similarity but also significantly enhances our understanding of the human brain's capabilities in processing 3D visual information. Project page at: https://jianxgao.github.io/MinD-3D.

Deep learning-based segmentation of the liver and hepatic lesions therein steadily gains relevance in clinical practice due to the increasing incidence of liver cancer each year. Whereas various network variants with overall promising results in the field of medical image segmentation have been successfully developed over the last years, almost all of them struggle with the challenge of accurately segmenting hepatic lesions in magnetic resonance imaging (MRI). This led to the idea of combining elements of convolutional and transformer-based architectures to overcome the existing limitations. This work presents a hybrid network called SWTR-Unet, consisting of a pretrained ResNet, transformer blocks as well as a common Unet-style decoder path. This network was primarily applied to single-modality non-contrast-enhanced liver MRI and additionally to the publicly available computed tomography (CT) data of the liver tumor segmentation (LiTS) challenge to verify the applicability on other modalities. For a broader evaluation, multiple state-of-the-art networks were implemented and applied, ensuring a direct comparability. Furthermore, correlation analysis and an ablation study were carried out, to investigate various influencing factors on the segmentation accuracy of the presented method. With Dice scores of averaged 98+-2% for liver and 81+-28% lesion segmentation on the MRI dataset and 97+-2% and 79+-25%, respectively on the CT dataset, the proposed SWTR-Unet proved to be a precise approach for liver and hepatic lesion segmentation with state-of-the-art results for MRI and competing accuracy in CT imaging. The achieved segmentation accuracy was found to be on par with manually performed expert segmentations as indicated by inter-observer variabilities for liver lesion segmentation. In conclusion, the presented method could save valuable time and resources in clinical practice.

Brain-to-image decoding has been recently propelled by the progress in generative AI models and the availability of large ultra-high field functional Magnetic Resonance Imaging (fMRI). However, current approaches depend on complicated multi-stage pipelines and preprocessing steps that typically collapse the temporal dimension of brain recordings, thereby limiting time-resolved brain decoders. Here, we introduce Dynadiff (Dynamic Neural Activity Diffusion for Image Reconstruction), a new single-stage diffusion model designed for reconstructing images from dynamically evolving fMRI recordings. Our approach offers three main contributions. First, Dynadiff simplifies training as compared to existing approaches. Second, our model outperforms state-of-the-art models on time-resolved fMRI signals, especially on high-level semantic image reconstruction metrics, while remaining competitive on preprocessed fMRI data that collapse time. Third, this approach allows a precise characterization of the evolution of image representations in brain activity. Overall, this work lays the foundation for time-resolved brain-to-image decoding.

Prostate cancer, a growing global health concern, necessitates precise diagnostic tools, with Magnetic Resonance Imaging (MRI) offering high-resolution soft tissue imaging that significantly enhances diagnostic accuracy. Recent advancements in explainable AI and representation learning have significantly improved prostate cancer diagnosis by enabling automated and precise lesion classification. However, existing explainable AI methods, particularly those based on frameworks like generative adversarial networks (GANs), are predominantly developed for natural image generation, and their application to medical imaging often leads to suboptimal performance due to the unique characteristics and complexity of medical image. To address these challenges, our paper introduces three key contributions. First, we propose ProjectedEx, a generative framework that provides interpretable, multi-attribute explanations, effectively linking medical image features to classifier decisions. Second, we enhance the encoder module by incorporating feature pyramids, which enables multiscale feedback to refine the latent space and improves the quality of generated explanations. Additionally, we conduct comprehensive experiments on both the generator and classifier, demonstrating the clinical relevance and effectiveness of ProjectedEx in enhancing interpretability and supporting the adoption of AI in medical settings. Code will be released at https://github.com/Richardqiyi/ProjectedEx

Brain decoding, a pivotal field in neuroscience, aims to reconstruct stimuli from acquired brain signals, primarily utilizing functional magnetic resonance imaging (fMRI). Currently, brain decoding is confined to a per-subject-per-model paradigm, limiting its applicability to the same individual for whom the decoding model is trained. This constraint stems from three key challenges: 1) the inherent variability in input dimensions across subjects due to differences in brain size; 2) the unique intrinsic neural patterns, influencing how different individuals perceive and process sensory information; 3) limited data availability for new subjects in real-world scenarios hampers the performance of decoding models. In this paper, we present a novel approach, MindBridge, that achieves cross-subject brain decoding by employing only one model. Our proposed framework establishes a generic paradigm capable of addressing these challenges by introducing biological-inspired aggregation function and novel cyclic fMRI reconstruction mechanism for subject-invariant representation learning. Notably, by cycle reconstruction of fMRI, MindBridge can enable novel fMRI synthesis, which also can serve as pseudo data augmentation. Within the framework, we also devise a novel reset-tuning method for adapting a pretrained model to a new subject. Experimental results demonstrate MindBridge's ability to reconstruct images for multiple subjects, which is competitive with dedicated subject-specific models. Furthermore, with limited data for a new subject, we achieve a high level of decoding accuracy, surpassing that of subject-specific models. This advancement in cross-subject brain decoding suggests promising directions for wider applications in neuroscience and indicates potential for more efficient utilization of limited fMRI data in real-world scenarios. Project page: https://littlepure2333.github.io/MindBridge

Glioblastomas are the most aggressive type of glioma, having a 5-year survival rate of 6.9%. Treatment typically involves surgery, followed by radiotherapy and chemotherapy, and frequent magnetic resonance imaging (MRI) scans to monitor disease progression. To assess treatment response, radiologists use the Response Assessment in Neuro-Oncology (RANO) criteria to categorize the tumor into one of four labels based on imaging and clinical features: complete response, partial response, stable disease, and progressive disease. This assessment is very complex and time-consuming. Since deep learning (DL) has been widely used to tackle classification problems, this work aimed to implement the first DL pipeline for the classification of RANO criteria based on two consecutive MRI acquisitions. The models were trained and tested on the open dataset LUMIERE. Five approaches were tested: 1) subtraction of input images, 2) different combinations of modalities, 3) different model architectures, 4) different pretraining tasks, and 5) adding clinical data. The pipeline that achieved the best performance used a Densenet264 considering only T1-weighted, T2-weighted, and Fluid Attenuated Inversion Recovery (FLAIR) images as input without any pretraining. A median Balanced Accuracy of 50.96% was achieved. Additionally, explainability methods were applied. Using Saliency Maps, the tumor region was often successfully highlighted. In contrast, Grad-CAM typically failed to highlight the tumor region, with some exceptions observed in the Complete Response and Progressive Disease classes, where it effectively identified the tumor region. These results set a benchmark for future studies on glioblastoma treatment response assessment based on the RANO criteria while emphasizing the heterogeneity of factors that might play a role when assessing the tumor's response to treatment.

Medical imaging is essential in modern radiotherapy, supporting diagnosis, treatment planning, and monitoring. Synthetic imaging, particularly synthetic computed tomography (sCT), is gaining traction in radiotherapy. The SynthRAD2025 dataset and Grand Challenge promote advancements in sCT generation by providing a benchmarking platform for algorithms using cone-beam CT (CBCT) and magnetic resonance imaging (MRI). The dataset includes 2362 cases: 890 MRI-CT and 1472 CBCT-CT pairs from head-and-neck, thoracic, and abdominal cancer patients treated at five European university medical centers (UMC Groningen, UMC Utrecht, Radboud UMC, LMU University Hospital Munich, and University Hospital of Cologne). Data were acquired with diverse scanners and protocols. Pre-processing, including rigid and deformable image registration, ensures high-quality, modality-aligned images. Extensive quality assurance validates image consistency and usability. All imaging data is provided in MetaImage (.mha) format, ensuring compatibility with medical image processing tools. Metadata, including acquisition parameters and registration details, is available in structured CSV files. To maintain dataset integrity, SynthRAD2025 is divided into training (65%), validation (10%), and test (25%) sets. The dataset is accessible at https://doi.org/10.5281/zenodo.14918089 under the SynthRAD2025 collection. This dataset supports benchmarking and the development of synthetic imaging techniques for radiotherapy applications. Use cases include sCT generation for MRI-only and MR-guided photon/proton therapy, CBCT-based dose calculations, and adaptive radiotherapy workflows. By integrating diverse acquisition settings, SynthRAD2025 fosters robust, generalizable image synthesis algorithms, advancing personalized cancer care and adaptive radiotherapy.

Clinically deployed deep learning-based segmentation models are known to fail on data outside of their training distributions. While clinicians review the segmentations, these models tend to perform well in most instances, which could exacerbate automation bias. Therefore, detecting out-of-distribution images at inference is critical to warn the clinicians that the model likely failed. This work applied the Mahalanobis distance (MD) post hoc to the bottleneck features of four Swin UNETR and nnU-net models that segmented the liver on T1-weighted magnetic resonance imaging and computed tomography. By reducing the dimensions of the bottleneck features with either principal component analysis or uniform manifold approximation and projection, images the models failed on were detected with high performance and minimal computational load. In addition, this work explored a non-parametric alternative to the MD, a k-th nearest neighbors distance (KNN). KNN drastically improved scalability and performance over MD when both were applied to raw and average-pooled bottleneck features.

In response to the global need for efficient early diagnosis of Autism Spectrum Disorder (ASD), this paper bridges the gap between traditional, time-consuming diagnostic methods and potential automated solutions. We propose a multi-atlas deep ensemble network, MADE-for-ASD, that integrates multiple atlases of the brain's functional magnetic resonance imaging (fMRI) data through a weighted deep ensemble network. Our approach integrates demographic information into the prediction workflow, which enhances ASD diagnosis performance and offers a more holistic perspective on patient profiling. We experiment with the well-known publicly available ABIDE (Autism Brain Imaging Data Exchange) I dataset, consisting of resting state fMRI data from 17 different laboratories around the globe. Our proposed system achieves 75.20% accuracy on the entire dataset and 96.40% on a specific subset - both surpassing reported ASD diagnosis accuracy in ABIDE I fMRI studies. Specifically, our model improves by 4.4 percentage points over prior works on the same amount of data. The model exhibits a sensitivity of 82.90% and a specificity of 69.70% on the entire dataset, and 91.00% and 99.50%, respectively, on the specific subset. We leverage the F-score to pinpoint the top 10 ROI in ASD diagnosis, such as precuneus and anterior cingulate/ventromedial. The proposed system can potentially pave the way for more cost-effective, efficient and scalable strategies in ASD diagnosis. Codes and evaluations are publicly available at https://github.com/hasan-rakibul/MADE-for-ASD.

Atrial fibrillation (AFib) is the prominent cardiac arrhythmia in the world. It affects mostly the elderly population, with potential consequences such as stroke and heart failure in the absence of necessary treatments as soon as possible. The importance of atrial scarring in the development and progression of AFib has gained recognition, positioning late gadolinium-enhanced magnetic resonance imaging (LGE-MRI) as a crucial technique for the non-invasive evaluation of atrial scar tissue. This review delves into the recent progress in segmenting atrial scars using LGE-MRIs, emphasizing the importance of precise scar measurement in the treatment and management of AFib. Initially, it provides a detailed examination of AFib. Subsequently, it explores the application of deep learning in this domain. The review culminates in a discussion of the latest research advancements in atrial scar segmentation using deep learning methods. By offering a thorough analysis of current technologies and their impact on AFib management strategies, this review highlights the integral role of deep learning in enhancing atrial scar segmentation and its implications for future therapeutic approaches.

The human brain is a complex, dynamic network, which is commonly studied using functional magnetic resonance imaging (fMRI) and modeled as network of Regions of interest (ROIs) for understanding various brain functions. Recent studies utilize deep learning approaches to learn the brain network representation based on functional connectivity (FC) profile, broadly falling into two main categories. The Fixed-FC approaches, utilizing the FC profile which represents the linear temporal relation within the brain network, are limited by failing to capture informative brain temporal dynamics. On the other hand, the Dynamic-FC approaches, modeling the evolving FC profile over time, often exhibit less satisfactory performance due to challenges in handling the inherent noisy nature of fMRI data. To address these challenges, we propose Brain Masked Auto-Encoder (BrainMAE) for learning representations directly from fMRI time-series data. Our approach incorporates two essential components: a region-aware graph attention mechanism designed to capture the relationships between different brain ROIs, and a novel self-supervised masked autoencoding framework for effective model pre-training. These components enable the model to capture rich temporal dynamics of brain activity while maintaining resilience to inherent noise in fMRI data. Our experiments demonstrate that BrainMAE consistently outperforms established baseline methods by significant margins in four distinct downstream tasks. Finally, leveraging the model's inherent interpretability, our analysis of model-generated representations reveals findings that resonate with ongoing research in the field of neuroscience.

Subsampling is commonly used to mitigate costs associated with data acquisition, such as time or energy requirements, motivating the development of algorithms for estimating the fully-sampled signal of interest x from partially observed measurements y. In maximum-entropy sampling, one selects measurement locations that are expected to have the highest entropy, so as to minimize uncertainty about x. This approach relies on an accurate model of the posterior distribution over future measurements, given the measurements observed so far. Recently, diffusion models have been shown to produce high-quality posterior samples of high-dimensional signals using guided diffusion. In this work, we propose Active Diffusion Subsampling (ADS), a method for performing active subsampling using guided diffusion in which the model tracks a distribution of beliefs over the true state of x throughout the reverse diffusion process, progressively decreasing its uncertainty by choosing to acquire measurements with maximum expected entropy, and ultimately generating the posterior distribution p(x | y). ADS can be applied using pre-trained diffusion models for any subsampling rate, and does not require task-specific retraining - just the specification of a measurement model. Furthermore, the maximum entropy sampling policy employed by ADS is interpretable, enhancing transparency relative to existing methods using black-box policies. Experimentally, we show that ADS outperforms fixed sampling strategies, and study an application of ADS in Magnetic Resonance Imaging acceleration using the fastMRI dataset, finding that ADS performs competitively with supervised methods. Code available at https://active-diffusion-subsampling.github.io/.

Understanding the hidden mechanisms behind human's visual perception is a fundamental question in neuroscience. To that end, investigating into the neural responses of human mind activities, such as functional Magnetic Resonance Imaging (fMRI), has been a significant research vehicle. However, analyzing fMRI signals is challenging, costly, daunting, and demanding for professional training. Despite remarkable progress in fMRI analysis, existing approaches are limited to generating 2D images and far away from being biologically meaningful and practically useful. Under this insight, we propose to generate visually plausible and functionally more comprehensive 3D outputs decoded from brain signals, enabling more sophisticated modeling of fMRI data. Conceptually, we reformulate this task as a {\em fMRI conditioned 3D object generation} problem. We design a novel 3D object representation learning method, Brain3D, that takes as input the fMRI data of a subject who was presented with a 2D image, and yields as output the corresponding 3D object images. The key capabilities of this model include tackling the noises with high-level semantic signals and a two-stage architecture design for progressive high-level information integration. Extensive experiments validate the superior capability of our model over previous state-of-the-art 3D object generation methods. Importantly, we show that our model captures the distinct functionalities of each region of human vision system as well as their intricate interplay relationships, aligning remarkably with the established discoveries in neuroscience. Further, preliminary evaluations indicate that Brain3D can successfully identify the disordered brain regions in simulated scenarios, such as V1, V2, V3, V4, and the medial temporal lobe (MTL) within the human visual system. Our data and code will be available at https://brain-3d.github.io/.

In the past five years, the use of generative and foundational AI systems has greatly improved the decoding of brain activity. Visual perception, in particular, can now be decoded from functional Magnetic Resonance Imaging (fMRI) with remarkable fidelity. This neuroimaging technique, however, suffers from a limited temporal resolution (approx0.5 Hz) and thus fundamentally constrains its real-time usage. Here, we propose an alternative approach based on magnetoencephalography (MEG), a neuroimaging device capable of measuring brain activity with high temporal resolution (approx5,000 Hz). For this, we develop an MEG decoding model trained with both contrastive and regression objectives and consisting of three modules: i) pretrained embeddings obtained from the image, ii) an MEG module trained end-to-end and iii) a pretrained image generator. Our results are threefold: Firstly, our MEG decoder shows a 7X improvement of image-retrieval over classic linear decoders. Second, late brain responses to images are best decoded with DINOv2, a recent foundational image model. Third, image retrievals and generations both suggest that high-level visual features can be decoded from MEG signals, although the same approach applied to 7T fMRI also recovers better low-level features. Overall, these results, while preliminary, provide an important step towards the decoding -- in real-time -- of the visual processes continuously unfolding within the human brain.

MRI super-resolution (SR) and denoising tasks are fundamental challenges in the field of deep learning, which have traditionally been treated as distinct tasks with separate paired training data. In this paper, we propose an innovative method that addresses both tasks simultaneously using a single deep learning model, eliminating the need for explicitly paired noisy and clean images during training. Our proposed model is primarily trained for SR, but also exhibits remarkable noise-cleaning capabilities in the super-resolved images. Instead of conventional approaches that introduce frequency-related operations into the generative process, our novel approach involves the use of a GAN model guided by a frequency-informed discriminator. To achieve this, we harness the power of the 3D Discrete Wavelet Transform (DWT) operation as a frequency constraint within the GAN framework for the SR task on magnetic resonance imaging (MRI) data. Specifically, our contributions include: 1) a 3D generator based on residual-in-residual connected blocks; 2) the integration of the 3D DWT with 1times 1 convolution into a DWT+conv unit within a 3D Unet for the discriminator; 3) the use of the trained model for high-quality image SR, accompanied by an intrinsic denoising process. We dub the model "Denoising Induced Super-resolution GAN (DISGAN)" due to its dual effects of SR image generation and simultaneous denoising. Departing from the traditional approach of training SR and denoising tasks as separate models, our proposed DISGAN is trained only on the SR task, but also achieves exceptional performance in denoising. The model is trained on 3D MRI data from dozens of subjects from the Human Connectome Project (HCP) and further evaluated on previously unseen MRI data from subjects with brain tumours and epilepsy to assess its denoising and SR performance.

We present SURE-Score: an approach for learning score-based generative models using training samples corrupted by additive Gaussian noise. When a large training set of clean samples is available, solving inverse problems via score-based (diffusion) generative models trained on the underlying fully-sampled data distribution has recently been shown to outperform end-to-end supervised deep learning. In practice, such a large collection of training data may be prohibitively expensive to acquire in the first place. In this work, we present an approach for approximately learning a score-based generative model of the clean distribution, from noisy training data. We formulate and justify a novel loss function that leverages Stein's unbiased risk estimate to jointly denoise the data and learn the score function via denoising score matching, while using only the noisy samples. We demonstrate the generality of SURE-Score by learning priors and applying posterior sampling to ill-posed inverse problems in two practical applications from different domains: compressive wireless multiple-input multiple-output channel estimation and accelerated 2D multi-coil magnetic resonance imaging reconstruction, where we demonstrate competitive reconstruction performance when learning at signal-to-noise ratio values of 0 and 10 dB, respectively.

Deep neural networks have enabled improved image quality and fast inference times for various inverse problems, including accelerated magnetic resonance imaging (MRI) reconstruction. However, such models require a large number of fully-sampled ground truth datasets, which are difficult to curate, and are sensitive to distribution drifts. In this work, we propose applying physics-driven data augmentations for consistency training that leverage our domain knowledge of the forward MRI data acquisition process and MRI physics to achieve improved label efficiency and robustness to clinically-relevant distribution drifts. Our approach, termed VORTEX, (1) demonstrates strong improvements over supervised baselines with and without data augmentation in robustness to signal-to-noise ratio change and motion corruption in data-limited regimes; (2) considerably outperforms state-of-the-art purely image-based data augmentation techniques and self-supervised reconstruction methods on both in-distribution and out-of-distribution data; and (3) enables composing heterogeneous image-based and physics-driven data augmentations. Our code is available at https://github.com/ad12/meddlr.

Convolutional neural networks (CNNs) are the current state-of-the-art meta-algorithm for volumetric segmentation of medical data, for example, to localize COVID-19 infected tissue on computer tomography scans or the detection of tumour volumes in magnetic resonance imaging. A key limitation of 3D CNNs on voxelised data is that the memory consumption grows cubically with the training data resolution. Occupancy networks (O-Nets) are an alternative for which the data is represented continuously in a function space and 3D shapes are learned as a continuous decision boundary. While O-Nets are significantly more memory efficient than 3D CNNs, they are limited to simple shapes, are relatively slow at inference, and have not yet been adapted for 3D semantic segmentation of medical data. Here, we propose Occupancy Networks for Semantic Segmentation (OSS-Nets) to accurately and memory-efficiently segment 3D medical data. We build upon the original O-Net with modifications for increased expressiveness leading to improved segmentation performance comparable to 3D CNNs, as well as modifications for faster inference. We leverage local observations to represent complex shapes and prior encoder predictions to expedite inference. We showcase OSS-Net's performance on 3D brain tumour and liver segmentation against a function space baseline (O-Net), a performance baseline (3D residual U-Net), and an efficiency baseline (2D residual U-Net). OSS-Net yields segmentation results similar to the performance baseline and superior to the function space and efficiency baselines. In terms of memory efficiency, OSS-Net consumes comparable amounts of memory as the function space baseline, somewhat more memory than the efficiency baseline and significantly less than the performance baseline. As such, OSS-Net enables memory-efficient and accurate 3D semantic segmentation that can scale to high resolutions.

Quantum computing promises to enhance machine learning and artificial intelligence. Different quantum algorithms have been proposed to improve a wide spectrum of machine learning tasks. Yet, recent theoretical works show that, similar to traditional classifiers based on deep classical neural networks, quantum classifiers would suffer from the vulnerability problem: adding tiny carefully-crafted perturbations to the legitimate original data samples would facilitate incorrect predictions at a notably high confidence level. This will pose serious problems for future quantum machine learning applications in safety and security-critical scenarios. Here, we report the first experimental demonstration of quantum adversarial learning with programmable superconducting qubits. We train quantum classifiers, which are built upon variational quantum circuits consisting of ten transmon qubits featuring average lifetimes of 150 mus, and average fidelities of simultaneous single- and two-qubit gates above 99.94% and 99.4% respectively, with both real-life images (e.g., medical magnetic resonance imaging scans) and quantum data. We demonstrate that these well-trained classifiers (with testing accuracy up to 99%) can be practically deceived by small adversarial perturbations, whereas an adversarial training process would significantly enhance their robustness to such perturbations. Our results reveal experimentally a crucial vulnerability aspect of quantum learning systems under adversarial scenarios and demonstrate an effective defense strategy against adversarial attacks, which provide a valuable guide for quantum artificial intelligence applications with both near-term and future quantum devices.

Accelerated magnetic resonance (MR) imaging attempts to reduce acquisition time by collecting data below the Nyquist rate. As an ill-posed inverse problem, many plausible solutions exist, yet the majority of deep learning approaches generate only a single solution. We instead focus on sampling from the posterior distribution, which provides more comprehensive information for downstream inference tasks. To do this, we design a novel conditional normalizing flow (CNF) that infers the signal component in the measurement operator's nullspace, which is later combined with measured data to form complete images. Using fastMRI brain and knee data, we demonstrate fast inference and accuracy that surpasses recent posterior sampling techniques for MRI. Code is available at https://github.com/jwen307/mri_cnf/

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where performance is highly sensitive to the differences in MR contrast, resolution, and orientation. This prevents broad applicability to diverse real-world clinical protocols. We introduce Brain-ID, an anatomical representation learning model for brain imaging. With the proposed "mild-to-severe" intra-subject generation, Brain-ID is robust to the subject-specific brain anatomy regardless of the appearance of acquired images (e.g., contrast, deformation, resolution, artifacts). Trained entirely on synthetic data, Brain-ID readily adapts to various downstream tasks through only one layer. We present new metrics to validate the intra- and inter-subject robustness of Brain-ID features, and evaluate their performance on four downstream applications, covering contrast-independent (anatomy reconstruction/contrast synthesis, brain segmentation), and contrast-dependent (super-resolution, bias field estimation) tasks. Extensive experiments on six public datasets demonstrate that Brain-ID achieves state-of-the-art performance in all tasks on different MRI modalities and CT, and more importantly, preserves its performance on low-resolution and small datasets. Code is available at https://github.com/peirong26/Brain-ID.

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where performance is highly sensitive to the differences in MR contrast, resolution, and orientation. This prevents broad applicability to diverse real-world clinical protocols. Here we introduce BrainFM, a modality-agnostic, multi-task vision foundation model for human brain imaging. With the proposed "mild-to-severe" intra-subject generation and "real-synth" mix-up training strategy, BrainFM is resilient to the appearance of acquired images (e.g., modality, contrast, deformation, resolution, artifacts), and can be directly applied to five fundamental brain imaging tasks, including image synthesis for CT and T1w/T2w/FLAIR MRI, anatomy segmentation, scalp-to-cortical distance, bias field estimation, and registration. We evaluate the efficacy of BrainFM on eleven public datasets, and demonstrate its robustness and effectiveness across all tasks and input modalities. Code is available at https://github.com/jhuldr/BrainFM.

Cardiac Magnetic Resonance (CMR) imaging serves as the gold-standard for evaluating cardiac morphology and function. Typically, a multi-view CMR stack, covering short-axis (SA) and 2/3/4-chamber long-axis (LA) views, is acquired for a thorough cardiac assessment. However, efficiently streamlining the complex, high-dimensional 3D+T CMR data and distilling compact, coherent representation remains a challenge. In this work, we introduce a whole-heart self-supervised learning framework that utilizes masked imaging modeling to automatically uncover the correlations between spatial and temporal patches throughout the cardiac stacks. This process facilitates the generation of meaningful and well-clustered heart representations without relying on the traditionally required, and often costly, labeled data. The learned heart representation can be directly used for various downstream tasks. Furthermore, our method demonstrates remarkable robustness, ensuring consistent representations even when certain CMR planes are missing/flawed. We train our model on 14,000 unlabeled CMR data from UK BioBank and evaluate it on 1,000 annotated data. The proposed method demonstrates superior performance to baselines in tasks that demand comprehensive 3D+T cardiac information, e.g. cardiac phenotype (ejection fraction and ventricle volume) prediction and multi-plane/multi-frame CMR segmentation, highlighting its effectiveness in extracting comprehensive cardiac features that are both anatomically and pathologically relevant.

Estimating the shape and motion state of the myocardium is essential in diagnosing cardiovascular diseases.However, cine magnetic resonance (CMR) imaging is dominated by 2D slices, whose large slice spacing challenges inter-slice shape reconstruction and motion acquisition.To address this problem, we propose a 4D reconstruction method that decouples motion and shape, which can predict the inter-/intra- shape and motion estimation from a given sparse point cloud sequence obtained from limited slices. Our framework comprises a neural motion model and an end-diastolic (ED) shape model. The implicit ED shape model can learn a continuous boundary and encourage the motion model to predict without the supervision of ground truth deformation, and the motion model enables canonical input of the shape model by deforming any point from any phase to the ED phase. Additionally, the constructed ED-space enables pre-training of the shape model, thereby guiding the motion model and addressing the issue of data scarcity. We propose the first 4D myocardial dataset as we know and verify our method on the proposed, public, and cross-modal datasets, showing superior reconstruction performance and enabling various clinical applications.

In the diverse field of medical imaging, automatic segmentation has numerous applications and must handle a wide variety of input domains, such as different types of Computed Tomography (CT) scans and Magnetic Resonance (MR) images. This heterogeneity challenges automatic segmentation algorithms to maintain consistent performance across different modalities due to the requirement for spatially aligned and paired images. Typically, segmentation models are trained using a single modality, which limits their ability to generalize to other types of input data without employing transfer learning techniques. Additionally, leveraging complementary information from different modalities to enhance segmentation precision often necessitates substantial modifications to popular encoder-decoder designs, such as introducing multiple branched encoding or decoding paths for each modality. In this work, we propose a simple Multi-Modal Segmentation (MulModSeg) strategy to enhance medical image segmentation across multiple modalities, specifically CT and MR. It incorporates two key designs: a modality-conditioned text embedding framework via a frozen text encoder that adds modality awareness to existing segmentation frameworks without significant structural modifications or computational overhead, and an alternating training procedure that facilitates the integration of essential features from unpaired CT and MR inputs. Through extensive experiments with both Fully Convolutional Network and Transformer-based backbones, MulModSeg consistently outperforms previous methods in segmenting abdominal multi-organ and cardiac substructures for both CT and MR modalities. The code is available in this {https://github.com/ChengyinLee/MulModSeg_2024{link}}.

The Circle of Willis (CoW) is an important network of arteries connecting major circulations of the brain. Its vascular architecture is believed to affect the risk, severity, and clinical outcome of serious neurovascular diseases. However, characterizing the highly variable CoW anatomy is still a manual and time-consuming expert task. The CoW is usually imaged by two non-invasive angiographic imaging modalities, magnetic resonance angiography (MRA) and computed tomography angiography (CTA), but there exist limited datasets with annotations on CoW anatomy, especially for CTA. Therefore, we organized the TopCoW challenge with the release of an annotated CoW dataset. The TopCoW dataset is the first public dataset with voxel-level annotations for 13 CoW vessel components, enabled by virtual reality technology. It is also the first large dataset using 200 pairs of MRA and CTA from the same patients. As part of the benchmark, we invited submissions worldwide and attracted over 250 registered participants from six continents. The submissions were evaluated on both internal and external test datasets of 226 scans from over five centers. The top performing teams achieved over 90% Dice scores at segmenting the CoW components, over 80% F1 scores at detecting key CoW components, and over 70% balanced accuracy at classifying CoW variants for nearly all test sets. The best algorithms also showed clinical potential in classifying fetal-type posterior cerebral artery and locating aneurysms with CoW anatomy. TopCoW demonstrated the utility and versatility of CoW segmentation algorithms for a wide range of downstream clinical applications with explainability. The annotated datasets and best performing algorithms have been released as public Zenodo records to foster further methodological development and clinical tool building.

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.

Brain MRI scans are often found in four modalities, consisting of T1-weighted with and without contrast enhancement (T1ce and T1w), T2-weighted imaging (T2w), and Flair. Leveraging complementary information from these different modalities enables models to learn richer, more discriminative features for understanding brain anatomy, which could be used in downstream tasks such as anomaly detection. However, in clinical practice, not all MRI modalities are always available due to various reasons. This makes missing modality generation a critical challenge in medical image analysis. In this paper, we propose SLaM-DiMM, a novel missing modality generation framework that harnesses the power of diffusion models to synthesize any of the four target MRI modalities from other available modalities. Our approach not only generates high-fidelity images but also ensures structural coherence across the depth of the volume through a dedicated coherence enhancement mechanism. Qualitative and quantitative evaluations on the BraTS-Lighthouse-2025 Challenge dataset demonstrate the effectiveness of the proposed approach in synthesizing anatomically plausible and structurally consistent results. Code is available at https://github.com/BheeshmSharma/SLaM-DiMM-MICCAI-BraTS-Challenge-2025.

Accelerating MRI scans is one of the principal outstanding problems in the MRI research community. Towards this goal, we hosted the second fastMRI competition targeted towards reconstructing MR images with subsampled k-space data. We provided participants with data from 7,299 clinical brain scans (de-identified via a HIPAA-compliant procedure by NYU Langone Health), holding back the fully-sampled data from 894 of these scans for challenge evaluation purposes. In contrast to the 2019 challenge, we focused our radiologist evaluations on pathological assessment in brain images. We also debuted a new Transfer track that required participants to submit models evaluated on MRI scanners from outside the training set. We received 19 submissions from eight different groups. Results showed one team scoring best in both SSIM scores and qualitative radiologist evaluations. We also performed analysis on alternative metrics to mitigate the effects of background noise and collected feedback from the participants to inform future challenges. Lastly, we identify common failure modes across the submissions, highlighting areas of need for future research in the MRI reconstruction community.

MRI is an inherently slow process, which leads to long scan time for high-resolution imaging. The speed of acquisition can be increased by ignoring parts of the data (undersampling). Consequently, this leads to the degradation of image quality, such as loss of resolution or introduction of image artefacts. This work aims to reconstruct highly undersampled Cartesian or radial MR acquisitions, with better resolution and with less to no artefact compared to conventional techniques like compressed sensing. In recent times, deep learning has emerged as a very important area of research and has shown immense potential in solving inverse problems, e.g. MR image reconstruction. In this paper, a deep learning based MR image reconstruction framework is proposed, which includes a modified regularised version of ResNet as the network backbone to remove artefacts from the undersampled image, followed by data consistency steps that fusions the network output with the data already available from undersampled k-space in order to further improve reconstruction quality. The performance of this framework for various undersampling patterns has also been tested, and it has been observed that the framework is robust to deal with various sampling patterns, even when mixed together while training, and results in very high quality reconstruction, in terms of high SSIM (highest being 0.990pm0.006 for acceleration factor of 3.5), while being compared with the fully sampled reconstruction. It has been shown that the proposed framework can successfully reconstruct even for an acceleration factor of 20 for Cartesian (0.968pm0.005) and 17 for radially (0.962pm0.012) sampled data. Furthermore, it has been shown that the framework preserves brain pathology during reconstruction while being trained on healthy subjects.

Self-supervised deep learning has accelerated 2D natural image analysis but remains difficult to translate into 3D MRI, where data are scarce and pre-trained 2D backbones cannot capture volumetric context. We present a sequence-invariant self-supervised framework leveraging quantitative MRI (qMRI). By simulating multiple MRI contrasts from a single 3D qMRI scan and enforcing consistent representations across these contrasts, we learn anatomy-centric rather than sequence-specific features. The result is a single 3D encoder that excels across tasks and protocols. Experiments on healthy brain segmentation (IXI), stroke lesion segmentation (ARC), and MRI denoising show significant gains over baseline SSL approaches, especially in low-data settings (up to +8.3\% Dice, +4.2 dB PSNR). It also generalises to unseen sites, supporting scalable clinical use. Code and trained models are publicly available at https://github.com/liamchalcroft/contrast-squared

Cardiac magnetic resonance (CMR) is a key investigation in clinical cardiovascular medicine and has been used extensively in population research. However, extracting clinically important measurements such as ejection fraction for diagnosing cardiovascular diseases remains time-consuming and subjective. We developed CineMA, a foundation AI model automating these tasks with limited labels. CineMA is a self-supervised autoencoder model trained on 74,916 cine CMR studies to reconstruct images from masked inputs. After fine-tuning, it was evaluated across eight datasets on 23 tasks from four categories: ventricle and myocardium segmentation, left and right ventricle ejection fraction calculation, disease detection and classification, and landmark localisation. CineMA is the first foundation model for cine CMR to match or outperform convolutional neural networks (CNNs). CineMA demonstrated greater label efficiency than CNNs, achieving comparable or better performance with fewer annotations. This reduces the burden of clinician labelling and supports replacing task-specific training with fine-tuning foundation models in future cardiac imaging applications. Models and code for pre-training and fine-tuning are available at https://github.com/mathpluscode/CineMA, democratising access to high-performance models that otherwise require substantial computational resources, promoting reproducibility and accelerating clinical translation.

Dynamic imaging is a beneficial tool for interventions to assess physiological changes. Nonetheless during dynamic MRI, while achieving a high temporal resolution, the spatial resolution is compromised. To overcome this spatio-temporal trade-off, this research presents a super-resolution (SR) MRI reconstruction with prior knowledge based fine-tuning to maximise spatial information while reducing the required scan-time for dynamic MRIs. An U-Net based network with perceptual loss is trained on a benchmark dataset and fine-tuned using one subject-specific static high resolution MRI as prior knowledge to obtain high resolution dynamic images during the inference stage. 3D dynamic data for three subjects were acquired with different parameters to test the generalisation capabilities of the network. The method was tested for different levels of in-plane undersampling for dynamic MRI. The reconstructed dynamic SR results after fine-tuning showed higher similarity with the high resolution ground-truth, while quantitatively achieving statistically significant improvement. The average SSIM of the lowest resolution experimented during this research (6.25~\% of the k-space) before and after fine-tuning were 0.939 pm 0.008 and 0.957 pm 0.006 respectively. This could theoretically result in an acceleration factor of 16, which can potentially be acquired in less than half a second. The proposed approach shows that the super-resolution MRI reconstruction with prior-information can alleviate the spatio-temporal trade-off in dynamic MRI, even for high acceleration factors.

This paper describes a novel nonparametric model for modeling diffusion MRI signals in q-space. In q-space, diffusion MRI signal is measured for a sequence of magnetic strengths (b-values) and magnetic gradient directions (b-vectors). We propose a Poly-RBF model, which employs a bidirectional framework with polynomial bases to model the signal along the b-value direction and Gaussian radial bases across the b-vectors. The model can accommodate sparse data on b-values and moderately dense data on b-vectors. The utility of Poly-RBF is inspected for two applications: 1) prediction of the dMRI signal, and 2) harmonization of dMRI data collected under different acquisition protocols with different scanners. Our results indicate that the proposed Poly-RBF model can more accurately predict the unmeasured diffusion signal than its competitors such as the Gaussian process model in {\tt Eddy} of FSL. Applying it to harmonizing the diffusion signal can significantly improve the reproducibility of derived white matter microstructure measures.

Machine Learning methods can learn how to reconstruct Magnetic Resonance Images and thereby accelerate acquisition, which is of paramount importance to the clinical workflow. Physics-informed networks incorporate the forward model of accelerated MRI reconstruction in the learning process. With increasing network complexity, robustness is not ensured when reconstructing data unseen during training. We aim to embed data consistency (DC) in deep networks while balancing the degree of network complexity. While doing so, we will assess whether either explicit or implicit enforcement of DC in varying network architectures is preferred to optimize performance. We propose a scheme called Cascades of Independently Recurrent Inference Machines (CIRIM) to assess DC through unrolled optimization. Herein we assess DC both implicitly by gradient descent and explicitly by a designed term. Extensive comparison of the CIRIM to CS as well as to other methods is performed: the E2EVN, CascadeNet, KIKINet, LPDNet, RIM, IRIM, and UNet. Models were trained and evaluated on T1-weighted and FLAIR contrast brain data, and T2-weighted knee data. Both 1D and 2D undersampling patterns were evaluated. Robustness was tested by reconstructing 7.5x prospectively undersampled 3D FLAIR MRI data of Multiple Sclerosis (MS) patients with white matter lesions. The CIRIM performed best when implicitly enforcing DC, while the E2EVN required an explicit DC formulation. In reconstructing MS patient data, prospectively acquired with a sampling pattern unseen during model training, the CIRIM maintained lesion contrast while efficiently denoising the images. The CIRIM showed highly promising generalization capabilities maintaining a very fair trade-off between reconstructed image quality and fast reconstruction times, which is crucial in the clinical workflow.

Typical quantitative MRI (qMRI) methods estimate parameter maps after image reconstructing, which is prone to biases and error propagation. We propose a Nonlinear Conjugate Gradient (NLCG) optimizer for model-based T2/T1 estimation, which incorporates U-Net regularization trained in a scan-specific manner. This end-to-end method directly estimates qMRI maps from undersampled k-space data using mono-exponential signal modeling with zero-shot scan-specific neural network regularization to enable high fidelity T1 and T2 mapping. T2 and T1 mapping results demonstrate the ability of the proposed NLCG-Net to improve estimation quality compared to subspace reconstruction at high accelerations.

Lack of large expert annotated MR datasets makes training deep learning models difficult. Therefore, a cross-modality (MR-CT) deep learning segmentation approach that augments training data using pseudo MR images produced by transforming expert-segmented CT images was developed. Eighty-One T2-weighted MRI scans from 28 patients with non-small cell lung cancers were analyzed. Cross-modality prior encoding the transformation of CT to pseudo MR images resembling T2w MRI was learned as a generative adversarial deep learning model. This model augmented training data arising from 6 expert-segmented T2w MR patient scans with 377 pseudo MRI from non-small cell lung cancer CT patient scans with obtained from the Cancer Imaging Archive. A two-dimensional Unet implemented with batch normalization was trained to segment the tumors from T2w MRI. This method was benchmarked against (a) standard data augmentation and two state-of-the art cross-modality pseudo MR-based augmentation and (b) two segmentation networks. Segmentation accuracy was computed using Dice similarity coefficient (DSC), Hausdroff distance metrics, and volume ratio. The proposed approach produced the lowest statistical variability in the intensity distribution between pseudo and T2w MR images measured as Kullback-Leibler divergence of 0.069. This method produced the highest segmentation accuracy with a DSC of 0.75 and the lowest Hausdroff distance on the test dataset. This approach produced highly similar estimations of tumor growth as an expert (P = 0.37). A novel deep learning MR segmentation was developed that overcomes the limitation of learning robust models from small datasets by leveraging learned cross-modality priors to augment training. The results show the feasibility of the approach and the corresponding improvement over the state-of-the-art methods.

We, team AImsterdam, summarize our submission to the fastMRI challenge (Zbontar et al., 2018). Our approach builds on recent advances in invertible learning to infer models as presented in Putzky and Welling (2019). Both, our single-coil and our multi-coil model share the same basic architecture.

Objective: To allow efficient learning using the Recurrent Inference Machine (RIM) for image reconstruction whereas not being strictly dependent on the training data distribution so that unseen modalities and pathologies are still accurately recovered. Methods: Theoretically, the RIM learns to solve the inverse problem of accelerated-MRI reconstruction whereas being robust to variable imaging conditions. The efficiency and generalization capabilities with different training datasets were studied, as well as recurrent network units with decreasing complexity: the Gated Recurrent Unit (GRU), the Minimal Gated Unit (MGU), and the Independently Recurrent Neural Network (IndRNN), to reduce inference times. Validation was performed against Compressed Sensing (CS) and further assessed based on data unseen during training. A pathology study was conducted by reconstructing simulated white matter lesions and prospectively undersampled data of a Multiple Sclerosis patient. Results: Training on a single modality of 3T T_1-weighted brain data appeared sufficient to also reconstruct 7T T_{2}^*-weighted brain and 3T T_2-weighted knee data. The IndRNN is an efficient recurrent unit, reducing inference time by 68\% compared to CS, whereas maintaining performance. The RIM was able to reconstruct lesions unseen during training more accurately than CS when trained on T_2-weighted knee data. Training on T_1-weighted brain data and on combined data slightly enhanced the signal compared to CS. Conclusion: The RIM is efficient when decreasing its complexity, which reduces the inference time, whereas still being able to reconstruct data and pathology that was unseen during training.

Compressed Sensing (CS) significantly speeds up Magnetic Resonance Image (MRI) processing and achieves accurate MRI reconstruction from under-sampled k-space data. According to the current research, there are still several problems with dynamic MRI k-space reconstruction based on CS. 1) There are differences between the Fourier domain and the Image domain, and the differences between MRI processing of different domains need to be considered. 2) As three-dimensional data, dynamic MRI has its spatial-temporal characteristics, which need to calculate the difference and consistency of surface textures while preserving structural integrity and uniqueness. 3) Dynamic MRI reconstruction is time-consuming and computationally resource-dependent. In this paper, we propose a novel robust low-rank dynamic MRI reconstruction optimization model via highly under-sampled and Discrete Fourier Transform (DFT) called the Robust Depth Linear Error Decomposition Model (RDLEDM). Our method mainly includes linear decomposition, double Total Variation (TV), and double Nuclear Norm (NN) regularizations. By adding linear image domain error analysis, the noise is reduced after under-sampled and DFT processing, and the anti-interference ability of the algorithm is enhanced. Double TV and NN regularizations can utilize both spatial-temporal characteristics and explore the complementary relationship between different dimensions in dynamic MRI sequences. In addition, Due to the non-smoothness and non-convexity of TV and NN terms, it is difficult to optimize the unified objective model. To address this issue, we utilize a fast algorithm by solving a primal-dual form of the original problem. Compared with five state-of-the-art methods, extensive experiments on dynamic MRI data demonstrate the superior performance of the proposed method in terms of both reconstruction accuracy and time complexity.

Dynamic MRI is a technique of acquiring a series of images continuously to follow the physiological changes over time. However, such fast imaging results in low resolution images. In this work, abdominal deformation model computed from dynamic low resolution images have been applied to high resolution image, acquired previously, to generate dynamic high resolution MRI. Dynamic low resolution images were simulated into different breathing phases (inhale and exhale). Then, the image registration between breathing time points was performed using the B-spline SyN deformable model and using cross-correlation as a similarity metric. The deformation model between different breathing phases were estimated from highly undersampled data. This deformation model was then applied to the high resolution images to obtain high resolution images of different breathing phases. The results indicated that the deformation model could be computed from relatively very low resolution images.

Compressed Sensing MRI reconstructs images of the body's internal anatomy from undersampled measurements, thereby reducing scan time. Recently, deep learning has shown great potential for reconstructing high-fidelity images from highly undersampled measurements. However, one needs to train multiple models for different undersampling patterns and desired output image resolutions, since most networks operate on a fixed discretization. Such approaches are highly impractical in clinical settings, where undersampling patterns and image resolutions are frequently changed to accommodate different real-time imaging and diagnostic requirements. We propose a unified MRI reconstruction model robust to various measurement undersampling patterns and image resolutions. Our approach uses neural operators, a discretization-agnostic architecture applied in both image and measurement spaces, to capture local and global features. Empirically, our model improves SSIM by 11% and PSNR by 4 dB over a state-of-the-art CNN (End-to-End VarNet), with 600times faster inference than diffusion methods. The resolution-agnostic design also enables zero-shot super-resolution and extended field-of-view reconstruction, offering a versatile and efficient solution for clinical MR imaging. Our unified model offers a versatile solution for MRI, adapting seamlessly to various measurement undersampling and imaging resolutions, making it highly effective for flexible and reliable clinical imaging. Our code is available at https://armeet.ca/nomri.

Quantitative susceptibility maps from magnetic resonance images can provide both prognostic and diagnostic information in multiple sclerosis, a neurodegenerative disease characterized by the formation of lesions in white matter brain tissue. In particular, susceptibility maps provide adequate contrast to distinguish between "rim" lesions, surrounded by deposited paramagnetic iron, and "non-rim" lesion types. These paramagnetic rim lesions (PRLs) are an emerging biomarker in multiple sclerosis. Much effort has been devoted to both detection and segmentation of such lesions to monitor longitudinal change. As paramagnetic rim lesions are rare, addressing this problem requires confronting the class imbalance between rim and non-rim lesions. We produce synthetic quantitative susceptibility maps of paramagnetic rim lesions and show that inclusion of such synthetic data improves classifier performance and provide a multi-channel extension to generate accompanying contrasts and probabilistic segmentation maps. We exploit the projection capability of our trained generative network to demonstrate a novel denoising approach that allows us to train on ambiguous rim cases and substantially increase the minority class. We show that both synthetic lesion synthesis and our proposed rim lesion label denoising method best approximate the unseen rim lesion distribution and improve detection in a clinically interpretable manner. We release our code and generated data at https://github.com/agr78/PRLx-GAN upon publication.

In MRI, motion artefacts are among the most common types of artefacts. They can degrade images and render them unusable for accurate diagnosis. Traditional methods, such as prospective or retrospective motion correction, have been proposed to avoid or alleviate motion artefacts. Recently, several other methods based on deep learning approaches have been proposed to solve this problem. This work proposes to enhance the performance of existing deep learning models by the inclusion of additional information present as image priors. The proposed approach has shown promising results and will be further investigated for clinical validity.

Motion artefacts in magnetic resonance brain images can have a strong impact on diagnostic confidence. The assessment of MR image quality is fundamental before proceeding with the clinical diagnosis. Motion artefacts can alter the delineation of structures such as the brain, lesions or tumours and may require a repeat scan. Otherwise, an inaccurate (e.g. correct pathology but wrong severity) or incorrect diagnosis (e.g. wrong pathology) may occur. "Image quality assessment" as a fast, automated step right after scanning can assist in deciding if the acquired images are diagnostically sufficient. An automated image quality assessment based on the structural similarity index (SSIM) regression through a residual neural network is proposed in this work. Additionally, a classification into different groups - by subdividing with SSIM ranges - is evaluated. Importantly, this method predicts SSIM values of an input image in the absence of a reference ground truth image. The networks were able to detect motion artefacts, and the best performance for the regression and classification task has always been achieved with ResNet-18 with contrast augmentation. The mean and standard deviation of residuals' distribution were mu=-0.0009 and sigma=0.0139, respectively. Whilst for the classification task in 3, 5 and 10 classes, the best accuracies were 97, 95 and 89\%, respectively. The results show that the proposed method could be a tool for supporting neuro-radiologists and radiographers in evaluating image quality quickly.

Cardiac MRI allows for a comprehensive assessment of myocardial structure, function, and tissue characteristics. Here we describe a foundational vision system for cardiac MRI, capable of representing the breadth of human cardiovascular disease and health. Our deep learning model is trained via self-supervised contrastive learning, by which visual concepts in cine-sequence cardiac MRI scans are learned from the raw text of the accompanying radiology reports. We train and evaluate our model on data from four large academic clinical institutions in the United States. We additionally showcase the performance of our models on the UK BioBank, and two additional publicly available external datasets. We explore emergent zero-shot capabilities of our system, and demonstrate remarkable performance across a range of tasks; including the problem of left ventricular ejection fraction regression, and the diagnosis of 35 different conditions such as cardiac amyloidosis and hypertrophic cardiomyopathy. We show that our deep learning system is capable of not only understanding the staggering complexity of human cardiovascular disease, but can be directed towards clinical problems of interest yielding impressive, clinical grade diagnostic accuracy with a fraction of the training data typically required for such tasks.

Cardiac MRI, crucial for evaluating heart structure and function, faces limitations like slow imaging and motion artifacts. Undersampling reconstruction, especially data-driven algorithms, has emerged as a promising solution to accelerate scans and enhance imaging performance using highly under-sampled data. Nevertheless, the scarcity of publicly available cardiac k-space datasets and evaluation platform hinder the development of data-driven reconstruction algorithms. To address this issue, we organized the Cardiac MRI Reconstruction Challenge (CMRxRecon) in 2023, in collaboration with the 26th International Conference on MICCAI. CMRxRecon presented an extensive k-space dataset comprising cine and mapping raw data, accompanied by detailed annotations of cardiac anatomical structures. With overwhelming participation, the challenge attracted more than 285 teams and over 600 participants. Among them, 22 teams successfully submitted Docker containers for the testing phase, with 7 teams submitted for both cine and mapping tasks. All teams use deep learning based approaches, indicating that deep learning has predominately become a promising solution for the problem. The first-place winner of both tasks utilizes the E2E-VarNet architecture as backbones. In contrast, U-Net is still the most popular backbone for both multi-coil and single-coil reconstructions. This paper provides a comprehensive overview of the challenge design, presents a summary of the submitted results, reviews the employed methods, and offers an in-depth discussion that aims to inspire future advancements in cardiac MRI reconstruction models. The summary emphasizes the effective strategies observed in Cardiac MRI reconstruction, including backbone architecture, loss function, pre-processing techniques, physical modeling, and model complexity, thereby providing valuable insights for further developments in this field.

Resection and whole brain radiotherapy (WBRT) are the standards of care for the treatment of patients with brain metastases (BM) but are often associated with cognitive side effects. Stereotactic radiosurgery (SRS) involves a more targeted treatment approach and has been shown to avoid the side effects associated with WBRT. However, SRS requires precise identification and delineation of BM. While many AI algorithms have been developed for this purpose, their clinical adoption has been limited due to poor model performance in the clinical setting. Major reasons for non-generalizable algorithms are the limitations in the datasets used for training the AI network. The purpose of this study was to create a large, heterogenous, annotated BM dataset for training and validation of AI models to improve generalizability. We present a BM dataset of 200 patients with pretreatment T1, T1 post-contrast, T2, and FLAIR MR images. The dataset includes contrast-enhancing and necrotic 3D segmentations on T1 post-contrast and whole tumor (including peritumoral edema) 3D segmentations on FLAIR. Our dataset contains 975 contrast-enhancing lesions, many of which are sub centimeter, along with clinical and imaging feature information. We used a streamlined approach to database-building leveraging a PACS-integrated segmentation workflow.

Accurate prediction of knee osteoarthritis (KOA) progression from structural MRI has a potential to enhance disease understanding and support clinical trials. Prior art focused on manually designed imaging biomarkers, which may not fully exploit all disease-related information present in MRI scan. In contrast, our method learns relevant representations from raw data end-to-end using Deep Learning, and uses them for progression prediction. The method employs a 2D CNN to process the data slice-wise and aggregate the extracted features using a Transformer. Evaluated on a large cohort (n=4,866), the proposed method outperforms conventional 2D and 3D CNN-based models and achieves average precision of 0.58pm0.03 and ROC AUC of 0.78pm0.01. This paper sets a baseline on end-to-end KOA progression prediction from structural MRI. Our code is publicly available at https://github.com/MIPT-Oulu/OAProgressionMR.

Purpose: To introduce a deep learning model capable of multi-organ segmentation in MRI scans, offering a solution to the current limitations in MRI analysis due to challenges in resolution, standardized intensity values, and variability in sequences. Materials and Methods: he model was trained on 1,200 manually annotated MRI scans from the UK Biobank, 221 in-house MRI scans and 1228 CT scans, leveraging cross-modality transfer learning from CT segmentation models. A human-in-the-loop annotation workflow was employed to efficiently create high-quality segmentations. The model's performance was evaluated on NAKO and the AMOS22 dataset containing 600 and 60 MRI examinations. Dice Similarity Coefficient (DSC) and Hausdorff Distance (HD) was used to assess segmentation accuracy. The model will be open sourced. Results: The model showcased high accuracy in segmenting well-defined organs, achieving Dice Similarity Coefficient (DSC) scores of 0.97 for the right and left lungs, and 0.95 for the heart. It also demonstrated robustness in organs like the liver (DSC: 0.96) and kidneys (DSC: 0.95 left, 0.95 right), which present more variability. However, segmentation of smaller and complex structures such as the portal and splenic veins (DSC: 0.54) and adrenal glands (DSC: 0.65 left, 0.61 right) revealed the need for further model optimization. Conclusion: The proposed model is a robust, tool for accurate segmentation of 40 anatomical structures in MRI and CT images. By leveraging cross-modality learning and interactive annotation, the model achieves strong performance and generalizability across diverse datasets, making it a valuable resource for researchers and clinicians. It is open source and can be downloaded from https://github.com/hhaentze/MRSegmentator.

Medical image retrieval is essential for clinical decision-making and translational research, relying on discriminative visual representations. Yet, current methods remain fragmented, relying on separate architectures and training strategies for 2D, 3D, and video-based medical data. This modality-specific design hampers scalability and inhibits the development of unified representations. To enable unified learning, we curate a large-scale hybrid-modality dataset comprising 867,653 medical imaging samples, including 2D X-rays and ultrasounds, RGB endoscopy videos, and 3D CT scans. Leveraging this dataset, we train M3Ret, a unified visual encoder without any modality-specific customization. It successfully learns transferable representations using both generative (MAE) and contrastive (SimDINO) self-supervised learning (SSL) paradigms. Our approach sets a new state-of-the-art in zero-shot image-to-image retrieval across all individual modalities, surpassing strong baselines such as DINOv3 and the text-supervised BMC-CLIP. More remarkably, strong cross-modal alignment emerges without paired data, and the model generalizes to unseen MRI tasks, despite never observing MRI during pretraining, demonstrating the generalizability of purely visual self-supervision to unseen modalities. Comprehensive analyses further validate the scalability of our framework across model and data sizes. These findings deliver a promising signal to the medical imaging community, positioning M3Ret as a step toward foundation models for visual SSL in multimodal medical image understanding.

Gliomas are aggressive brain tumors that require accurate imaging-based diagnosis, with segmentation playing a critical role in evaluating morphology and treatment decisions. Manual delineation of gliomas is time-consuming and prone to variability, motivating the use of deep learning to improve consistency and alleviate clinical workload. However, existing methods often fail to fully exploit the information available in multi-parametric MRI (mp-MRI), particularly inter-slice contextual features, and typically require considerable computational resources while lacking robustness across tumor type variations. We present GBT-SAM, a parameter-efficient deep learning framework that adapts the Segment Anything Model (SAM), a large-scale vision model, to volumetric mp-MRI data. GBT-SAM reduces input complexity by selecting fewer than 2.6\% of slices per scan while incorporating all four MRI modalities, preserving essential tumor-related information with minimal cost. Furthermore, our model is trained by a two-step fine-tuning strategy that incorporates a depth-aware module to capture inter-slice correlations and lightweight adaptation layers, resulting in just 6.5M trainable parameters, which is the lowest among SAM-based approaches. GBT-SAM achieves a Dice Score of 93.54 on the BraTS Adult Glioma dataset and demonstrates robust performance on Meningioma, Pediatric Glioma, and Sub-Saharan Glioma datasets. These results highlight GBT-SAM's potential as a computationally efficient and domain-robust framework for brain tumor segmentation using mp-MRI. Our code and models are available at https://github.com/vpulab/med-sam-brain .

Deep learning (DL) has shown promise for faster, high quality accelerated MRI reconstruction. However, supervised DL methods depend on extensive amounts of fully-sampled (labeled) data and are sensitive to out-of-distribution (OOD) shifts, particularly low signal-to-noise ratio (SNR) acquisitions. To alleviate this challenge, we propose Noise2Recon, a model-agnostic, consistency training method for joint MRI reconstruction and denoising that can use both fully-sampled (labeled) and undersampled (unlabeled) scans in semi-supervised and self-supervised settings. With limited or no labeled training data, Noise2Recon outperforms compressed sensing and deep learning baselines, including supervised networks, augmentation-based training, fine-tuned denoisers, and self-supervised methods, and matches performance of supervised models, which were trained with 14x more fully-sampled scans. Noise2Recon also outperforms all baselines, including state-of-the-art fine-tuning and augmentation techniques, among low-SNR scans and when generalizing to other OOD factors, such as changes in acceleration factors and different datasets. Augmentation extent and loss weighting hyperparameters had negligible impact on Noise2Recon compared to supervised methods, which may indicate increased training stability. Our code is available at https://github.com/ad12/meddlr.

Medical image arbitrary-scale super-resolution (MIASSR) has recently gained widespread attention, aiming to super sample medical volumes at arbitrary scales via a single model. However, existing MIASSR methods face two major limitations: (i) reliance on high-resolution (HR) volumes and (ii) limited generalization ability, which restricts their application in various scenarios. To overcome these limitations, we propose Cube-based Neural Radiance Field (CuNeRF), a zero-shot MIASSR framework that can yield medical images at arbitrary scales and viewpoints in a continuous domain. Unlike existing MIASSR methods that fit the mapping between low-resolution (LR) and HR volumes, CuNeRF focuses on building a coordinate-intensity continuous representation from LR volumes without the need for HR references. This is achieved by the proposed differentiable modules: including cube-based sampling, isotropic volume rendering, and cube-based hierarchical rendering. Through extensive experiments on magnetic resource imaging (MRI) and computed tomography (CT) modalities, we demonstrate that CuNeRF outperforms state-of-the-art MIASSR methods. CuNeRF yields better visual verisimilitude and reduces aliasing artifacts at various upsampling factors. Moreover, our CuNeRF does not need any LR-HR training pairs, which is more flexible and easier to be used than others. Our code will be publicly available soon.

In MRI, images of the same contrast (e.g., T_1) from the same subject can exhibit noticeable differences when acquired using different hardware, sequences, or scan parameters. These differences in images create a domain gap that needs to be bridged by a step called image harmonization, to process the images successfully using conventional or deep learning-based image analysis (e.g., segmentation). Several methods, including deep learning-based approaches, have been proposed to achieve image harmonization. However, they often require datasets from multiple domains for deep learning training and may still be unsuccessful when applied to images from unseen domains. To address this limitation, we propose a novel concept called `Blind Harmonization', which utilizes only target domain data for training but still has the capability to harmonize images from unseen domains. For the implementation of blind harmonization, we developed BlindHarmony using an unconditional flow model trained on target domain data. The harmonized image is optimized to have a correlation with the input source domain image while ensuring that the latent vector of the flow model is close to the center of the Gaussian distribution. BlindHarmony was evaluated on both simulated and real datasets and compared to conventional methods. BlindHarmony demonstrated noticeable performance on both datasets, highlighting its potential for future use in clinical settings. The source code is available at: https://github.com/SNU-LIST/BlindHarmony

Solving the inverse problem is the key step in evaluating the capacity of a physical model to describe real phenomena. In medical image computing, it aligns with the classical theme of image-based model personalization. Traditionally, a solution to the problem is obtained by performing either sampling or variational inference based methods. Both approaches aim to identify a set of free physical model parameters that results in a simulation best matching an empirical observation. When applied to brain tumor modeling, one of the instances of image-based model personalization in medical image computing, the overarching drawback of the methods is the time complexity for finding such a set. In a clinical setting with limited time between imaging and diagnosis or even intervention, this time complexity may prove critical. As the history of quantitative science is the history of compression, we align in this paper with the historical tendency and propose a method compressing complex traditional strategies for solving an inverse problem into a simple database query task. We evaluated different ways of performing the database query task assessing the trade-off between accuracy and execution time. On the exemplary task of brain tumor growth modeling, we prove that the proposed method achieves one order speed-up compared to existing approaches for solving the inverse problem. The resulting compute time offers critical means for relying on more complex and, hence, realistic models, for integrating image preprocessing and inverse modeling even deeper, or for implementing the current model into a clinical workflow.

In this work, we address the TrackRAD2025 challenge of real-time tumor tracking in cine-MRI sequences of the thoracic and abdominal regions under strong data scarcity constraints. Two complementary strategies were explored: (i) unsupervised registration with the IMPACT similarity metric and (ii) foundation model-based segmentation leveraging SAM 2.1 and its recent variants through prompt-based interaction. Due to the one-second runtime constraint, the SAM-based method was ultimately selected. The final configuration used SAM2.1 b+ with mask-based prompts from the first annotated slice, fine-tuned solely on the small labeled subset from TrackRAD2025. Training was configured to minimize overfitting, using 1024x1024 patches (batch size 1), standard augmentations, and a balanced Dice + IoU loss. A low uniform learning rate (0.0001) was applied to all modules (prompt encoder, decoder, Hiera backbone) to preserve generalization while adapting to annotator-specific styles. Training lasted 300 epochs (~12h on RTX A6000, 48GB). The same inference strategy was consistently applied across all anatomical sites and MRI field strengths. Test-time augmentation was considered but ultimately discarded due to negligible performance gains. The final model was selected based on the highest Dice Similarity Coefficient achieved on the validation set after fine-tuning. On the hidden test set, the model reached a Dice score of 0.8794, ranking 6th overall in the TrackRAD2025 challenge. These results highlight the strong potential of foundation models for accurate and real-time tumor tracking in MRI-guided radiotherapy.

The PI-CAI (Prostate Imaging: Cancer AI) challenge led to expert-level diagnostic algorithms for clinically significant prostate cancer detection. The algorithms receive biparametric MRI scans as input, which consist of T2-weighted and diffusion-weighted scans. These scans can be misaligned due to multiple factors in the scanning process. Image registration can alleviate this issue by predicting the deformation between the sequences. We investigate the effect of image registration on the diagnostic performance of AI-based prostate cancer diagnosis. First, the image registration algorithm, developed in MeVisLab, is analyzed using a dataset with paired lesion annotations. Second, the effect on diagnosis is evaluated by comparing case-level cancer diagnosis performance between using the original dataset, rigidly aligned diffusion-weighted scans, or deformably aligned diffusion-weighted scans. Rigid registration showed no improvement. Deformable registration demonstrated a substantial improvement in lesion overlap (+10% median Dice score) and a positive yet non-significant improvement in diagnostic performance (+0.3% AUROC, p=0.18). Our investigation shows that a substantial improvement in lesion alignment does not directly lead to a significant improvement in diagnostic performance. Qualitative analysis indicated that jointly developing image registration methods and diagnostic AI algorithms could enhance diagnostic accuracy and patient outcomes.

Multimodal models trained on large natural image-text pair datasets have exhibited astounding abilities in generating high-quality images. Medical imaging data is fundamentally different to natural images, and the language used to succinctly capture relevant details in medical data uses a different, narrow but semantically rich, domain-specific vocabulary. Not surprisingly, multi-modal models trained on natural image-text pairs do not tend to generalize well to the medical domain. Developing generative imaging models faithfully representing medical concepts while providing compositional diversity could mitigate the existing paucity of high-quality, annotated medical imaging datasets. In this work, we develop a strategy to overcome the large natural-medical distributional shift by adapting a pre-trained latent diffusion model on a corpus of publicly available chest x-rays (CXR) and their corresponding radiology (text) reports. We investigate the model's ability to generate high-fidelity, diverse synthetic CXR conditioned on text prompts. We assess the model outputs quantitatively using image quality metrics, and evaluate image quality and text-image alignment by human domain experts. We present evidence that the resulting model (RoentGen) is able to create visually convincing, diverse synthetic CXR images, and that the output can be controlled to a new extent by using free-form text prompts including radiology-specific language. Fine-tuning this model on a fixed training set and using it as a data augmentation method, we measure a 5% improvement of a classifier trained jointly on synthetic and real images, and a 3% improvement when trained on a larger but purely synthetic training set. Finally, we observe that this fine-tuning distills in-domain knowledge in the text-encoder and can improve its representation capabilities of certain diseases like pneumothorax by 25%.

The burgeoning integration of 3D medical imaging into healthcare has led to a substantial increase in the workload of medical professionals. To assist clinicians in their diagnostic processes and alleviate their workload, the development of a robust system for retrieving similar case studies presents a viable solution. While the concept holds great promise, the field of 3D medical text-image retrieval is currently limited by the absence of robust evaluation benchmarks and curated datasets. To remedy this, our study presents a groundbreaking dataset, BIMCV-R (This dataset will be released upon acceptance.), which includes an extensive collection of 8,069 3D CT volumes, encompassing over 2 million slices, paired with their respective radiological reports. Expanding upon the foundational work of our dataset, we craft a retrieval strategy, MedFinder. This approach employs a dual-stream network architecture, harnessing the potential of large language models to advance the field of medical image retrieval beyond existing text-image retrieval solutions. It marks our preliminary step towards developing a system capable of facilitating text-to-image, image-to-text, and keyword-based retrieval tasks.

Cerebrovascular disease often requires multiple imaging modalities for accurate diagnosis, treatment, and monitoring. Computed Tomography Angiography (CTA) and Time-of-Flight Magnetic Resonance Angiography (TOF-MRA) are two common non-invasive angiography techniques, each with distinct strengths in accessibility, safety, and diagnostic accuracy. While CTA is more widely used in acute stroke due to its faster acquisition times and higher diagnostic accuracy, TOF-MRA is preferred for its safety, as it avoids radiation exposure and contrast agent-related health risks. Despite the predominant role of CTA in clinical workflows, there is a scarcity of open-source CTA data, limiting the research and development of AI models for tasks such as large vessel occlusion detection and aneurysm segmentation. This study explores diffusion-based image-to-image translation models to generate synthetic CTA images from TOF-MRA input. We demonstrate the modality conversion from TOF-MRA to CTA and show that diffusion models outperform a traditional U-Net-based approach. Our work compares different state-of-the-art diffusion architectures and samplers, offering recommendations for optimal model performance in this cross-modality translation task.

Developing advanced medical imaging retrieval systems is challenging due to the varying definitions of `similar images' across different medical contexts. This challenge is compounded by the lack of large-scale, high-quality medical imaging retrieval datasets and benchmarks. In this paper, we propose a novel methodology that leverages dense radiology reports to define image-wise similarity ordering at multiple granularities in a scalable and fully automatic manner. Using this approach, we construct two comprehensive medical imaging retrieval datasets: MIMIC-IR for Chest X-rays and CTRATE-IR for CT scans, providing detailed image-image ranking annotations conditioned on diverse anatomical structures. Furthermore, we develop two retrieval systems, RadIR-CXR and model-ChestCT, which demonstrate superior performance in traditional image-image and image-report retrieval tasks. These systems also enable flexible, effective image retrieval conditioned on specific anatomical structures described in text, achieving state-of-the-art results on 77 out of 78 metrics.

We present a new neural network, the XPDNet, for MRI reconstruction from periodically under-sampled multi-coil data. We inform the design of this network by taking best practices from MRI reconstruction and computer vision. We show that this network can achieve state-of-the-art reconstruction results, as shown by its ranking of second in the fastMRI 2020 challenge.

Automated radiology report generation offers an effective solution to alleviate radiologists' workload. However, most existing methods focus primarily on single or fixed-view images to model current disease conditions, which limits diagnostic accuracy and overlooks disease progression. Although some approaches utilize longitudinal data to track disease progression, they still rely on single images to analyze current visits. To address these issues, we propose enhanced contrastive learning with Multi-view Longitudinal data to facilitate chest X-ray Report Generation, named MLRG. Specifically, we introduce a multi-view longitudinal contrastive learning method that integrates spatial information from current multi-view images and temporal information from longitudinal data. This method also utilizes the inherent spatiotemporal information of radiology reports to supervise the pre-training of visual and textual representations. Subsequently, we present a tokenized absence encoding technique to flexibly handle missing patient-specific prior knowledge, allowing the model to produce more accurate radiology reports based on available prior knowledge. Extensive experiments on MIMIC-CXR, MIMIC-ABN, and Two-view CXR datasets demonstrate that our MLRG outperforms recent state-of-the-art methods, achieving a 2.3% BLEU-4 improvement on MIMIC-CXR, a 5.5% F1 score improvement on MIMIC-ABN, and a 2.7% F1 RadGraph improvement on Two-view CXR.

Image registration is the process of bringing different images into a common coordinate system - a technique widely used in various applications of computer vision, such as remote sensing, image retrieval, and, most commonly, medical imaging. Deep learning based techniques have been applied successfully to tackle various complex medical image processing problems, including medical image registration. Over the years, several image registration techniques have been proposed using deep learning. Deformable image registration techniques such as Voxelmorph have been successful in capturing finer changes and providing smoother deformations. However, Voxelmorph, as well as ICNet and FIRE, do not explicitly encode global dependencies (i.e. the overall anatomical view of the supplied image) and, therefore, cannot track large deformations. In order to tackle the aforementioned problems, this paper extends the Voxelmorph approach in three different ways. To improve the performance in case of small as well as large deformations, supervision of the model at different resolutions has been integrated using a multi-scale UNet. To support the network to learn and encode the minute structural co-relations of the given image-pairs, a self-constructing graph network (SCGNet) has been used as the latent of the multi-scale UNet - which can improve the learning process of the model and help the model to generalise better. And finally, to make the deformations inverse-consistent, cycle consistency loss has been employed. On the task of registration of brain MRIs, the proposed method achieved significant improvements over ANTs and VoxelMorph, obtaining a Dice score of 0.8013 \pm 0.0243 for intramodal and 0.6211 \pm 0.0309 for intermodal, while VoxelMorph achieved 0.7747 \pm 0.0260 and 0.6071 \pm 0.0510, respectively

Cervical disc herniation (CDH) is a prevalent musculoskeletal disorder that significantly impacts health and requires labor-intensive analysis from experts. Despite advancements in automated detection of medical imaging, two significant challenges hinder the real-world application of these methods. First, the computational complexity and resource demands present a significant gap for real-time application. Second, noise in MRI reduces the effectiveness of existing methods by distorting feature extraction. To address these challenges, we propose three key contributions: Firstly, we introduced MedDet, which leverages the multi-teacher single-student knowledge distillation for model compression and efficiency, meanwhile integrating generative adversarial training to enhance performance. Additionally, we customize the second-order nmODE to improve the model's resistance to noise in MRI. Lastly, we conducted comprehensive experiments on the CDH-1848 dataset, achieving up to a 5% improvement in mAP compared to previous methods. Our approach also delivers over 5 times faster inference speed, with approximately 67.8% reduction in parameters and 36.9% reduction in FLOPs compared to the teacher model. These advancements significantly enhance the performance and efficiency of automated CDH detection, demonstrating promising potential for future application in clinical practice. See project website https://steve-zeyu-zhang.github.io/MedDet

Image registration is fundamental in medical imaging, enabling precise alignment of anatomical structures for diagnosis, treatment planning, image-guided treatment or longitudinal monitoring. This work introduces IMPACT (Image Metric with Pretrained model-Agnostic Comparison for Transmodality registration), a generic semantic similarity metric designed for seamless integration into diverse image registration frameworks (such as Elastix and Voxelmorph). It compares deep learning-based features extracted from medical images without requiring task-specific training, ensuring broad applicability across various modalities. By leveraging the features of the large-scale pretrained TotalSegmentator models and the ability to integrate Segment Anything Model (SAM) and other large-scale segmentation networks, this approach offers significant advantages. It provides robust, scalable, and efficient solutions for multimodal image registration. The IMPACT loss was evaluated on five challenging registration tasks involving thoracic CT/CBCT, and pelvic MR/CT datasets. Quantitative metrics, such as Target Registration Error and Dice Similarity Coefficient, demonstrated significant improvements in anatomical alignment compared to baseline methods. Qualitative analyses further confirmed the increased robustness of the proposed metric in the face of noise, artifacts, and modality variations. IMPACT's versatility and efficiency make it a valuable tool for advancing registration performance in clinical and research applications, addressing critical challenges in multimodal medical imaging.

Radiography imaging protocols focus on particular body regions, therefore producing images of great similarity and yielding recurrent anatomical structures across patients. To exploit this structured information, we propose the use of Space-aware Memory Queues for In-painting and Detecting anomalies from radiography images (abbreviated as SQUID). We show that SQUID can taxonomize the ingrained anatomical structures into recurrent patterns; and in the inference, it can identify anomalies (unseen/modified patterns) in the image. SQUID surpasses 13 state-of-the-art methods in unsupervised anomaly detection by at least 5 points on two chest X-ray benchmark datasets measured by the Area Under the Curve (AUC). Additionally, we have created a new dataset (DigitAnatomy), which synthesizes the spatial correlation and consistent shape in chest anatomy. We hope DigitAnatomy can prompt the development, evaluation, and interpretability of anomaly detection methods.

Ultra-high-field 7T MRI offers enhanced spatial resolution and tissue contrast that enables the detection of subtle pathological changes in neurological disorders. However, the limited availability of 7T scanners restricts widespread clinical adoption due to substantial infrastructure costs and technical demands. Computational approaches for synthesizing 7T-quality images from accessible 3T acquisitions present a viable solution to this accessibility challenge. Existing CNN approaches suffer from limited spatial coverage, while Transformer models demand excessive computational overhead. RWKV architectures offer an efficient alternative for global feature modeling in medical image synthesis, combining linear computational complexity with strong long-range dependency capture. Building on this foundation, we propose Frequency Spatial-RWKV (FS-RWKV), an RWKV-based framework for 3T-to-7T MRI translation. To better address the challenges of anatomical detail preservation and global tissue contrast recovery, FS-RWKV incorporates two key modules: (1) Frequency-Spatial Omnidirectional Shift (FSO-Shift), which performs discrete wavelet decomposition followed by omnidirectional spatial shifting on the low-frequency branch to enhance global contextual representation while preserving high-frequency anatomical details; and (2) Structural Fidelity Enhancement Block (SFEB), a module that adaptively reinforces anatomical structure through frequency-aware feature fusion. Comprehensive experiments on UNC and BNU datasets demonstrate that FS-RWKV consistently outperforms existing CNN-, Transformer-, GAN-, and RWKV-based baselines across both T1w and T2w modalities, achieving superior anatomical fidelity and perceptual quality.

Purpose: In radiology, large language models (LLMs), including ChatGPT, have recently gained attention, and their utility is being rapidly evaluated. However, concerns have emerged regarding their reliability in clinical applications due to limitations such as hallucinations and insufficient referencing. To address these issues, we focus on the latest technology, retrieval-augmented generation (RAG), which enables LLMs to reference reliable external knowledge (REK). Specifically, this study examines the utility and reliability of a recently released RAG-equipped LLM (RAG-LLM), NotebookLM, for staging lung cancer. Materials and methods: We summarized the current lung cancer staging guideline in Japan and provided this as REK to NotebookLM. We then tasked NotebookLM with staging 100 fictional lung cancer cases based on CT findings and evaluated its accuracy. For comparison, we performed the same task using a gold-standard LLM, GPT-4 Omni (GPT-4o), both with and without the REK. Results: NotebookLM achieved 86% diagnostic accuracy in the lung cancer staging experiment, outperforming GPT-4o, which recorded 39% accuracy with the REK and 25% without it. Moreover, NotebookLM demonstrated 95% accuracy in searching reference locations within the REK. Conclusion: NotebookLM successfully performed lung cancer staging by utilizing the REK, demonstrating superior performance compared to GPT-4o. Additionally, it provided highly accurate reference locations within the REK, allowing radiologists to efficiently evaluate the reliability of NotebookLM's responses and detect possible hallucinations. Overall, this study highlights the potential of NotebookLM, a RAG-LLM, in image diagnosis.

Purpose: Medical imaging has become increasingly important in diagnosing and treating oncological patients, particularly in radiotherapy. Recent advances in synthetic computed tomography (sCT) generation have increased interest in public challenges to provide data and evaluation metrics for comparing different approaches openly. This paper describes a dataset of brain and pelvis computed tomography (CT) images with rigidly registered CBCT and MRI images to facilitate the development and evaluation of sCT generation for radiotherapy planning. Acquisition and validation methods: The dataset consists of CT, CBCT, and MRI of 540 brains and 540 pelvic radiotherapy patients from three Dutch university medical centers. Subjects' ages ranged from 3 to 93 years, with a mean age of 60. Various scanner models and acquisition settings were used across patients from the three data-providing centers. Details are available in CSV files provided with the datasets. Data format and usage notes: The data is available on Zenodo (https://doi.org/10.5281/zenodo.7260705) under the SynthRAD2023 collection. The images for each subject are available in nifti format. Potential applications: This dataset will enable the evaluation and development of image synthesis algorithms for radiotherapy purposes on a realistic multi-center dataset with varying acquisition protocols. Synthetic CT generation has numerous applications in radiation therapy, including diagnosis, treatment planning, treatment monitoring, and surgical planning.

Multimodal MRI provides critical complementary information for accurate brain tumor segmentation. However, conventional methods struggle when certain modalities are missing due to issues such as image quality, protocol inconsistencies, patient allergies, or financial constraints. To address this, we propose a robust single-modality parallel processing framework that achieves high segmentation accuracy even with incomplete modalities. Leveraging Holder divergence and mutual information, our model maintains modality-specific features while dynamically adjusting network parameters based on the available inputs. By using these divergence- and information-based loss functions, the framework effectively quantifies discrepancies between predictions and ground-truth labels, resulting in consistently accurate segmentation. Extensive evaluations on the BraTS 2018 and BraTS 2020 datasets demonstrate superior performance over existing methods in handling missing modalities.

Medical image segmentation has recently demonstrated impressive progress with deep neural networks, yet the heterogeneous modalities and scarcity of mask annotations limit the development of segmentation models on unannotated modalities. This paper investigates a new paradigm for leveraging generative models in medical applications: controllably synthesizing data for unannotated modalities, without requiring registered data pairs. Specifically, we make the following contributions in this paper: (i) we collect and curate a large-scale radiology image-text dataset, MedGen-1M, comprising modality labels, attributes, region, and organ information, along with a subset of organ mask annotations, to support research in controllable medical image generation; (ii) we propose a diffusion-based data engine, termed MRGen, which enables generation conditioned on text prompts and masks, synthesizing MR images for diverse modalities lacking mask annotations, to train segmentation models on unannotated modalities; (iii) we conduct extensive experiments across various modalities, illustrating that our data engine can effectively synthesize training samples and extend MRI segmentation towards unannotated modalities.

Medical imaging is critical to the diagnosis and treatment of numerous medical problems, including many forms of cancer. Medical imaging reports distill the findings and observations of radiologists, creating an unstructured textual representation of unstructured medical images. Large-scale use of this text-encoded information requires converting the unstructured text to a structured, semantic representation. We explore the extraction and normalization of anatomical information in radiology reports that is associated with radiological findings. We investigate this extraction and normalization task using a span-based relation extraction model that jointly extracts entities and relations using BERT. This work examines the factors that influence extraction and normalization performance, including the body part/organ system, frequency of occurrence, span length, and span diversity. It discusses approaches for improving performance and creating high-quality semantic representations of radiological phenomena.

Industry standards require medical device manufacturers to perform implant-induced artefact testing in phantoms at a pre-clinical stage to define the extent of artefacts that can be expected during MRI. Once a device is commercially available, studies on volunteers, cadavers or patients are performed to investigate implant-induced artefacts and artefact reduction methods more in-depth. This study describes the design and evaluation of a realistic head phantom for pre-clinical implant-induced artefact testing in a relevant environment. A case study is performed where a state-of-the-art piezoelectric bone conduction implant is used in the 1.5 T and 3 T MRI environments. Images were acquired using clinical and novel metal artefact reducing (MARS) sequences at both field strengths. Artefact width and length were measured in a healthy volunteer and compared with artefact sizes obtained in the phantom. Artefact sizes are reported that are similar in shape between the phantom and a volunteer, yet with dimensions differing up to 20% between both. When the implant magnet is removed, the artefact size can be reduced below a diameter of 5 cm, whilst the presence of an implant magnet and splint creates higher artefacts up to 20 cm in diameter. Pulse sequences have been altered to reduce the scan time up to 7 minutes, while preserving the image quality. These results show that the anthropomorphic phantom can be used at a preclinical stage to provide clinically relevant images, illustrating the impact of the artefact on important brain structures.

X-ray imaging is a rapid and cost-effective tool for visualizing internal human anatomy. While multi-view X-ray imaging provides complementary information that enhances diagnosis, intervention, and education, acquiring images from multiple angles increases radiation exposure and complicates clinical workflows. To address these challenges, we propose a novel view-conditioned diffusion model for synthesizing multi-view X-ray images from a single view. Unlike prior methods, which are limited in angular range, resolution, and image quality, our approach leverages the Diffusion Transformer to preserve fine details and employs a weak-to-strong training strategy for stable high-resolution image generation. Experimental results demonstrate that our method generates higher-resolution outputs with improved control over viewing angles. This capability has significant implications not only for clinical applications but also for medical education and data extension, enabling the creation of diverse, high-quality datasets for training and analysis. Our code is available at https://github.com/xiechun298/SV-DRR.

While deep networks have achieved broad success in analyzing natural images, when applied to medical scans, they often fail in unexcepted situations. We investigate this challenge and focus on model sensitivity to domain shifts, such as data sampled from different hospitals or data confounded by demographic variables such as sex, race, etc, in the context of chest X-rays and skin lesion images. A key finding we show empirically is that existing visual backbones lack an appropriate prior from the architecture for reliable generalization in these settings. Taking inspiration from medical training, we propose giving deep networks a prior grounded in explicit medical knowledge communicated in natural language. To this end, we introduce Knowledge-enhanced Bottlenecks (KnoBo), a class of concept bottleneck models that incorporates knowledge priors that constrain it to reason with clinically relevant factors found in medical textbooks or PubMed. KnoBo uses retrieval-augmented language models to design an appropriate concept space paired with an automatic training procedure for recognizing the concept. We evaluate different resources of knowledge and recognition architectures on a broad range of domain shifts across 20 datasets. In our comprehensive evaluation with two imaging modalities, KnoBo outperforms fine-tuned models on confounded datasets by 32.4% on average. Finally, evaluations reveal that PubMed is a promising resource for making medical models less sensitive to domain shift, outperforming other resources on both diversity of information and final prediction performance.

The integration of neural-network-based systems into clinical practice is limited by challenges related to domain generalization and robustness. The computer vision community established benchmarks such as ImageNet-C as a fundamental prerequisite to measure progress towards those challenges. Similar datasets are largely absent in the medical imaging community which lacks a comprehensive benchmark that spans across imaging modalities and applications. To address this gap, we create and open-source MedMNIST-C, a benchmark dataset based on the MedMNIST+ collection covering 12 datasets and 9 imaging modalities. We simulate task and modality-specific image corruptions of varying severity to comprehensively evaluate the robustness of established algorithms against real-world artifacts and distribution shifts. We further provide quantitative evidence that our simple-to-use artificial corruptions allow for highly performant, lightweight data augmentation to enhance model robustness. Unlike traditional, generic augmentation strategies, our approach leverages domain knowledge, exhibiting significantly higher robustness when compared to widely adopted methods. By introducing MedMNIST-C and open-sourcing the corresponding library allowing for targeted data augmentations, we contribute to the development of increasingly robust methods tailored to the challenges of medical imaging. The code is available at https://github.com/francescodisalvo05/medmnistc-api .

Transforming two-dimensional (2D) images into three-dimensional (3D) volumes is a well-known yet challenging problem for the computer vision community. In the medical domain, a few previous studies attempted to convert two or more input radiographs into computed tomography (CT) volumes. Following their effort, we introduce a diffusion model-based technology that can rotate the anatomical content of any input radiograph in 3D space, potentially enabling the visualization of the entire anatomical content of the radiograph from any viewpoint in 3D. Similar to previous studies, we used CT volumes to create Digitally Reconstructed Radiographs (DRRs) as the training data for our model. However, we addressed two significant limitations encountered in previous studies: 1. We utilized conditional diffusion models with classifier-free guidance instead of Generative Adversarial Networks (GANs) to achieve higher mode coverage and improved output image quality, with the only trade-off being slower inference time, which is often less critical in medical applications; and 2. We demonstrated that the unreliable output of style transfer deep learning (DL) models, such as Cycle-GAN, to transfer the style of actual radiographs to DRRs could be replaced with a simple yet effective training transformation that randomly changes the pixel intensity histograms of the input and ground-truth imaging data during training. This transformation makes the diffusion model agnostic to any distribution variations of the input data pixel intensity, enabling the reliable training of a DL model on input DRRs and applying the exact same model to conventional radiographs (or DRRs) during inference.