Magnetic Resonance Imaging (MRI) is an essential diagnostic tool for assessing knee injuries. However, manual interpretation of MRI slices remains time-consuming and prone to inter-observer variability. This study presents a systematic evaluation of various deep learning architectures combined with explainable AI (xAI) techniques for automated region of interest (ROI) detection in knee MRI scans. We investigate both supervised and self-supervised approaches, including ResNet50, InceptionV3, Vision Transformers (ViT), and multiple U-Net variants augmented with multi-layer perceptron (MLP) classifiers. To enhance interpretability and clinical relevance, we integrate xAI methods such as Grad-CAM and Saliency Maps. Model performance is assessed using AUC for classification and PSNR/SSIM for reconstruction quality, along with qualitative ROI visualizations. Our results demonstrate that ResNet50 consistently excels in classification and ROI identification, outperforming transformer-based models under the constraints of the MRNet dataset. While hybrid U-Net + MLP approaches show potential for leveraging spatial features in reconstruction and interpretability, their classification performance remains lower. Grad-CAM consistently provided the most clinically meaningful explanations across architectures. Overall, CNN-based transfer learning emerges as the most effective approach for this dataset, while future work with larger-scale pretraining may better unlock the potential of transformer models.
BrainFusionNet: a deep learning and XAI model to understand local, global, and sequential features of MRI images for improved brain tumour detection
School of Mathematics, Physics and Computing, University of Southern Queensland（南方昆士兰大学数学、物理与计算学院）；School of Engineering, University of Southern Queensland（南方昆士兰大学工程学院）
Evaluation of Machine Learning Reconstruction Techniques for Accelerated Brain MRI Scans
Humber River Hospital（亨伯河医院）；Toronto Western Hospital, University of Toronto（多伦多大学多伦多西区医院）；Foqus Technologies Inc.（Foqus 技术公司）；Robarts Research Institute, Western University（西安大略大学罗巴茨研究所）
Istituto Italiano di Tecnologia（意大利理工学院）；Simon Fraser University（西蒙弗雷泽大学）；University of Verona（维罗纳大学）；Fondation Campus Biotech（生物科技园区基金会）；University of British Columbia（不列颠哥伦比亚大学）；Fondazione Bruno Kessler（布鲁诺·凯斯勒基金会）
This paper presents a simple and effective generalization method for magnetic resonance imaging (MRI) segmentation when data is collected from multiple MRI scanning sites and as a consequence is affected by (site-)domain shifts. We propose to integrate a traditional encoder-decoder network with a regularization network. This added network includes an auxiliary loss term which is responsible for the reduction of the domain shift problem and for the resulting improved generalization. The proposed method was evaluated on multiple sclerosis lesion segmentation from MRI data. We tested the proposed…
Reduced NEXI protocol for the quantification of human gray matter microstructure on the Connectome 2.0 scanner
Lausanne University Hospital (CHUV) and University of Lausanne（拉沃斯大学医院（CHUV）和拉沃斯大学）；Massachusetts General Hospital（麻省总医院）；Athinoula A. Martinos Center for Biomedical Imaging（阿提诺拉A.马丁诺斯生物医学成像中心）
Harvard Medical School（哈佛医学院）；Massachusetts General Hospital（麻省总医院）；California Institute of Technology（加州理工学院）；Massachusetts Institute of Technology（麻省理工学院）
In neuroimaging, MRI tissue properties characterize underlying neurobiology, provide quantitative biomarkers for neurological disease detection and analysis, and can be used to synthesize arbitrary MRI contrasts. Estimating tissue properties from a single scan session using a protocol available on all clinical scanners promises to reduce scan time and cost, enable quantitative analysis in routine clinical scans and provide scan-independent biomarkers of disease. However, existing tissue properties estimation methods - most often $\mathbf{T_1}$ relaxation, $\mathbf{T_2^*}$ relaxation, and proto…
Motion artefacts created by patient motion during an MRI scan occur frequently in practice, often rendering the scans clinically unusable and requiring a re-scan. While many methods have been employed to ameliorate the effects of patient motion, these often fall short in practice. In this paper we propose a novel method for removing motion artefacts using a deep neural network with two input branches that discriminates between patient poses using the motion's timing. The first branch receives a subset of the $k$-space data collected during a single patient pose, and the second branch receives …
Female-RHINO: A Real-Time Scanner-Integrated Framework for Automated Quantitative Uterine MRI Analysis and Structured Reporting
Radiologisches Institut, Universitätsklinikum Erlangen（埃朗根大学医院放射学研究所）；School of Biomedical Engineering and Imaging, KCL（KCL生物医学工程与成像学院）；Institute for Information Processing, Leibniz University Hannover（汉诺威莱布尼茨大学信息处理研究所）；CAIMed, L3S research institute（CAIMed，L3S研究机构）
Identification of lymph nodes (LN) in T2 Magnetic Resonance Imaging (MRI) is an important step performed by radiologists during the assessment of lymphoproliferative diseases. The size of the nodes play a crucial role in their staging, and radiologists sometimes use an additional contrast sequence such as diffusion weighted imaging (DWI) for confirmation. However, lymph nodes have diverse appearances in T2 MRI scans, making it tough to stage for metastasis. Furthermore, radiologists often miss smaller metastatic lymph nodes over the course of a busy day. To deal with these issues, we propose t…
Mohamed Bin Zayed University of Artificial Intelligence（穆罕默德·本·扎耶德人工智能大学）
Glioblastoma is a common brain malignancy that tends to occur in older adults and is almost always lethal. The effectiveness of chemotherapy, being the standard treatment for most cancer types, can be improved if a particular genetic sequence in the tumor known as MGMT promoter is methylated. However, to identify the state of the MGMT promoter, the conventional approach is to perform a biopsy for genetic analysis, which is time and effort consuming. A couple of recent publications proposed a connection between the MGMT promoter state and the MRI scans of the tumor and hence suggested the use o…
Parallel imaging is a widely-used technique to accelerate magnetic resonance imaging (MRI). However, current methods still perform poorly in reconstructing artifact-free MRI images from highly undersampled k-space data. Recently, implicit neural representation (INR) has emerged as a new deep learning paradigm for learning the internal continuity of an object. In this study, we adopted INR to parallel MRI reconstruction. The MRI image was modeled as a continuous function of spatial coordinates. This function was parameterized by a neural network and learned directly from the measured k-space it…
A generalisable head MRI defacing pipeline: Evaluation on 2,566 meningioma scans
School of Biomedical Engineering & Imaging Sciences, King’s College London（伦敦国王学院生物医学工程与成像科学学校）；Department of Neurosurgery, King’s College Hospital NHS Foundation Trust（伦敦国王学院医院神经外科部门）
Indian Institute of Technology Indore（印度理工学院印多尔分校）
Alzheimer's Disease (AD) is a neurodegenerative disease that is one of the significant causes of death in the elderly population. Many deep learning techniques have been proposed to diagnose AD using Magnetic Resonance Imaging (MRI) scans. Predicting AD using 2D slices extracted from 3D MRI scans is challenging as the inter-slice information gets lost. To this end, we propose a novel and lightweight framework termed 'Biceph-Net' for AD diagnosis using 2D MRI scans that model both the intra-slice and inter-slice information. Biceph-Net has been experimentally shown to perform similar to other S…
Tel Aviv Medical Center（特拉维夫医疗中心）；Tel Aviv University（特拉维夫大学）
Purpose: Repeated brain MRI scans are performed in many clinical scenarios, such as follow up of patients with tumors and therapy response assessment. In this paper, the authors show an approach to utilize former scans of the patient for the acceleration of repeated MRI scans. Methods: The proposed approach utilizes the possible similarity of the repeated scans in longitudinal MRI studies. Since similarity is not guaranteed, sampling and reconstruction are adjusted during acquisition to match the actual similarity between the scans. The baseline MR scan is utilized both in the sampling stage, …
A Scalable AI Driven, IoT Integrated Cognitive Digital Twin for Multi-Modal Neuro-Oncological Prognostics and Tumor Kinetics Prediction using Enhanced Vision Transformer and XAI
University of Calcutta（加尔各答大学）；Institute of Engineering and Management（工程与管理学院）；University of Engineering and Management（工程与管理大学）；San Francisco State University（旧金山州立大学）
Technical University of Denmark（丹麦技术大学）；icometrix（icometrix公司）；Technical University of Munich（慕尼黑工业大学）；University of Antwerp（安特卫普大学）；Harvard Medical School（哈佛医学院）
Most publicly available brain MRI datasets are very homogeneous in terms of scanner and protocols, and it is difficult for models that learn from such data to generalize to multi-center and multi-scanner data. We propose a novel data augmentation approach with the aim of approximating the variability in terms of intensities and contrasts present in real world clinical data. We use a Gaussian Mixture Model based approach to change tissue intensities individually, producing new contrasts while preserving anatomical information. We train a deep learning model on a single scanner dataset and evalu…
King’s College London（伦敦国王学院）；King’s College Hospital（国王学院医院）；Wrightington, Wigan and Leigh NHSFT（赖廷顿、维冈与利国家医疗服务基金会信托）；University College London（伦敦大学学院）
The growing demand for head magnetic resonance imaging (MRI) examinations, along with a global shortage of radiologists, has led to an increase in the time taken to report head MRI scans around the world. For many neurological conditions, this delay can result in increased morbidity and mortality. An automated triaging tool could reduce reporting times for abnormal examinations by identifying abnormalities at the time of imaging and prioritizing the reporting of these scans. In this work, we present a convolutional neural network for detecting clinically-relevant abnormalities in $\text{T}_2$-…
Massachusetts General Hospital（麻省总医院）；Harvard University（哈佛大学）；General Electric Healthcare（通用电气医疗集团）；Indian Institute of Science（印度科学学院）
Gliomas are one of the most frequent brain tumors and are classified into high grade and low grade gliomas. The segmentation of various regions such as tumor core, enhancing tumor etc. plays an important role in determining severity and prognosis. Here, we have developed a multi-threshold model based on attention U-Net for identification of various regions of the tumor in magnetic resonance imaging (MRI). We propose a multi-path segmentation and built three separate models for the different regions of interest. The proposed model achieved mean Dice Coefficient of 0.59, 0.72, and 0.61 for enhan…
University of Brescia（布雷西亚大学）；University of Glasgow（格拉斯哥大学）
Many functional and structural neuroimaging studies call for accurate morphometric segmentation of different brain structures starting from image intensity values of MRI scans. Current automatic (multi-) atlas-based segmentation strategies often lack accuracy on difficult-to-segment brain structures and, since these methods rely on atlas-to-scan alignment, they may take long processing times. Recently, methods deploying solutions based on Convolutional Neural Networks (CNNs) are making the direct analysis of out-of-the-scanner data feasible. However, current CNN-based solutions partition the t…
University of Karachi（卡拉奇大学）；Zhejiang University（浙江大学）；Iqra University（伊克拉大学）；Karachi Institute of Economics and Technology（卡拉奇经济与技术学院）；King Abdulaziz University（阿卜杜勒阿齐兹国王大学）
Heart is one of the vital organs of human body. A minor dysfunction of heart even for a short time interval can be fatal, therefore, efficient monitoring of its physiological state is essential for the patients with cardiovascular diseases. In the recent past, various computer assisted medical imaging systems have been proposed for the segmentation of the organ of interest. However, for the segmentation of heart using MRI, only few methods have been proposed each with its own merits and demerits. For further advancement in this area of research, we analyze automated heart segmentation methods …
Department of Electrical and Computer Engineering, University of Minnesota（明尼苏达大学电气与计算机工程系）
Long scan duration remains a challenge for high-resolution MRI. Deep learning has emerged as a powerful means for accelerated MRI reconstruction by providing data-driven regularizers that are directly learned from data. These data-driven priors typically remain unchanged for future data in the testing phase once they are learned during training. In this study, we propose to use a transfer learning approach to fine-tune these regularizers for new subjects using a self-supervision approach. While the proposed approach can compromise the extremely fast reconstruction time of deep learning MRI met…
Improve Cross-Modality Segmentation by Treating T1-Weighted MRI Images as Inverted CT Scans
Charité - Universitätsmedizin Berlin（柏林查理医院）；Freie Universität Berlin（柏林自由大学）；Humboldt Universität zu Berlin（柏林洪堡大学）；Radboud University Medical Center（拉德伯德大学医学中心）；Massachusetts General Hospital and Harvard Medical School（麻省总医院和哈佛医学院）；Technical University of Munich（慕尼黑技术大学）
Saarland University（萨尔兰大学）；DFKI（德国人工智能研究中心）；INRIA（法国国家信息与自动化研究所）；University of Edinburgh（爱丁堡大学）
We describe a minimally-supervised method for computing a statistical shape space model of the palate surface. The model is created from a corpus of volumetric magnetic resonance imaging (MRI) scans collected from 12 speakers. We extract a 3D mesh of the palate from each speaker, then train the model using principal component analysis (PCA). The palate model is then tested using 3D MRI from another corpus and evaluated using a high-resolution optical scan. We find that the error is low even when only a handful of measured coordinates are available. In both cases, our approach yields promising …
Mansoura University（曼苏拉大学）；Higher Institute of Engineering and Technology（高等工程技术学院）
Prostate cancer is the most dangerous cancer diagnosed in men worldwide. Prostate diagnosis has been affected by many factors, such as lesion complexity, observer visibility, and variability. Many techniques based on Magnetic Resonance Imaging (MRI) have been used for prostate cancer identification and classification in the last few decades. Developing these techniques is crucial and has a great medical effect because they improve the treatment benefits and the chance of patients' survival. A new technique that depends on MRI has been proposed to improve the diagnosis. This technique consists …
Structural magnetic resonance imaging (MRI) has been widely utilized for analysis and diagnosis of brain diseases. Automatic segmentation of brain tumors is a challenging task for computer-aided diagnosis due to low-tissue contrast in the tumor subregions. To overcome this, we devise a novel pixel-wise segmentation framework through a convolutional 3D to 2D MR patch conversion model to predict class labels of the central pixel in the input sliding patches. Precisely, we first extract 3D patches from each modality to calibrate slices through the squeeze and excitation (SE) block. Then, the outp…
A Review of Electromagnetic Elimination Methods for low-field portable MRI scanner
Harvard Medical School（哈佛医学院）；University of Michigan（密歇根大学）；Harvard University（哈佛大学）；New York University（纽约大学）；Columbia University（哥伦比亚大学）；Guangxi University（广西大学）
Recon-all-clinical: Cortical surface reconstruction and analysis of heterogeneous clinical brain MRI
Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）；Copenhagen University Hospital - Amager and Hvidovre（哥本哈根大学医院阿莫尔与维杜夫院区）；Danish Research Centre for Magnetic Resonance（丹麦磁共振研究中心）；Centre for Functional and Diagnostic Imaging and Research（功能与诊断成像及研究中心）
University of Stuttgart（斯图加特大学）；Max Planck Institute for Intelligent Systems（马克斯·普朗克智能系统研究所）
Age is an essential factor in modern diagnostic procedures. However, assessment of the true biological age (BA) remains a daunting task due to the lack of reference ground-truth labels. Current BA estimation approaches are either restricted to skeletal images or rely on non-imaging modalities that yield a whole-body BA assessment. However, various organ systems may exhibit different aging characteristics due to lifestyle and genetic factors. In this initial study, we propose a new framework for organ-specific BA estimation utilizing 3D magnetic resonance image (MRI) scans. As a first step, thi…
Recent studies suggest that combined analysis of Magnetic resonance imaging~(MRI) that measures brain atrophy and positron emission tomography~(PET) that quantifies hypo-metabolism provides improved accuracy in diagnosing Alzheimer's disease. However, such techniques are limited by the availability of corresponding scans of each modality. Current work focuses on a cross-modal approach to estimate FDG-PET scans for the given MR scans using a 3D U-Net architecture. The use of the complete MR image instead of a local patch based approach helps in capturing non-local and non-linear correlations be…
L-TGVN: Leveraging Longitudinal Priors for Personalized Rapid MRI
NYU Center for Data Science（纽约大学数据科学中心）；Center for Advanced Imaging Innovation and Research (CAI²R)（先进成像创新与研究中心）；Courant Institute of Mathematical Sciences（数学科学学院）；Function Health
The Rio Hortega University Hospital Glioblastoma dataset: a comprehensive collection of preoperative, early postoperative and recurrence MRI scans (RHUH-GBM)
Technical University of Munich（慕尼黑工业大学）；Ludwig-Maximilians-University Munich（慕尼黑路德维希-马克西米利安大学）
The reconstruction of cortical surfaces from brain magnetic resonance imaging (MRI) scans is essential for quantitative analyses of cortical thickness and sulcal morphology. Although traditional and deep learning-based algorithmic pipelines exist for this purpose, they have two major drawbacks: lengthy runtimes of multiple hours (traditional) or intricate post-processing, such as mesh extraction and topology correction (deep learning-based). In this work, we address both of these issues and propose Vox2Cortex, a deep learning-based algorithm that directly yields topologically correct, three-di…
University College London（伦敦大学学院）；Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）；Massachusetts Institute of Technology（麻省理工学院）
Every year, millions of brain MRI scans are acquired in hospitals, which is a figure considerably larger than the size of any research dataset. Therefore, the ability to analyse such scans could transform neuroimaging research. Yet, their potential remains untapped, since no automated algorithm is robust enough to cope with the high variability in clinical acquisitions (MR contrasts, resolutions, orientations, artefacts, subject populations). Here we present SynthSeg+, an AI segmentation suite that enables, for the first time, robust analysis of heterogeneous clinical datasets. In addition to …
University of Stuttgart（斯图加特大学）；University of Tübingen（图宾根大学）；King’s College London（伦敦国王学院）
Individuals age differently depending on a multitude of different factors such as lifestyle, medical history and genetics. Often, the global chronological age is not indicative of the true ageing process. An organ-based age estimation would yield a more accurate health state assessment. In this work, we propose a new deep learning architecture for organ-based age estimation based on magnetic resonance images (MRI). The proposed network is a 3D convolutional neural network (CNN) with increased depth and width made possible by the hybrid utilization of inception and fire modules. We apply the pr…
University of New South Wales（新南威尔士大学）；Neuroscience Research Australia (NeuRA)（澳大利亚神经科学研究所（NeuRA））
Semi-supervised learning has made significant progress in medical image segmentation. However, existing methods primarily utilize information acquired from a single dimensionality (2D/3D), resulting in sub-optimal performance on challenging data, such as magnetic resonance imaging (MRI) scans with multiple objects and highly anisotropic resolution. To address this issue, we present a Hybrid Dual Mean-Teacher (HD-Teacher) model with hybrid, semi-supervised, and multi-task learning to achieve highly effective semi-supervised segmentation. HD-Teacher employs a 2D and a 3D mean-teacher network to …
Institute of Smart Systems and Artificial Intelligence, Nazarbayev University（纳扎尔巴耶夫大学智能系统与人工智能研究所）
Alzheimer's disease (AD) is a progressive brain disorder that causes memory and functional impairments. The advances in machine learning and publicly available medical datasets initiated multiple studies in AD diagnosis. In this work, we utilize a multi-modal deep learning approach in classifying normal cognition, mild cognitive impairment and AD classes on the basis of structural MRI and diffusion tensor imaging (DTI) scans from the OASIS-3 dataset. In addition to a conventional multi-modal network, we also present an input agnostic architecture that allows diagnosis with either sMRI or DTI s…
Ibn Tofail University（伊本·托法勒大学）；Cheikh Anta Diop University（谢赫·安塔·迪奥普大学）；Abdelmalek Essaadi University（阿卜杜勒马利克·埃萨迪大学）
Fractal analysis has been shown to be useful in image processing for characterizing shape and gray-scale complexity. The fractal feature is a compact descriptor used to give a numerical measure of the degree of irregularity of the medical images. This descriptor property does not give ownership of the local image structure. In this paper, we present a combination of this parameter based on Box Counting with GLCM Features. This powerful combination has proved good results especially in classification of medical texture from MRI and CT Scan images of trabecular bone. This method has the potentia…
The MRI Scanner as a Diagnostic: Image-less Active Sampling
School of Engineering, The University of Edinburgh（爱丁堡大学工程学院）；Krannert Cardiovascular Research Center, Indiana University School of Medicine（印第安纳大学医学院克兰纳特心血管研究中心）；The Alan Turing Institute（阿兰·图灵研究所）
Vanderbilt University（范德堡大学）；Middle Tennessee State University（中田纳西州立大学）；University of Texas at Austin（德克萨斯大学奥斯汀分校）
Diffusion-weighted magnetic resonance imaging (DW-MRI) allows for non-invasive imaging of the local fiber architecture of the human brain at a millimetric scale. Multiple classical approaches have been proposed to detect both single (e.g., tensors) and multiple (e.g., constrained spherical deconvolution, CSD) fiber population orientations per voxel. However, existing techniques generally exhibit low reproducibility across MRI scanners. Herein, we propose a data-driven tech-nique using a neural network design which exploits two categories of data. First, training data were acquired on three squ…
School of Biomedical Engineering, King’s College London（伦敦国王学院生物医学工程学院）；King’s College Hospital（国王学院医院）；Institute of Psychiatry, Psychology & Neuroscience, King’s College London（伦敦国王学院精神病学、心理学与神经科学研究所）；Centre for Medical Image Computing, Dementia Research, University College London（伦敦大学学院医学影像计算中心（痴呆研究））
Labelling large datasets for training high-capacity neural networks is a major obstacle to the development of deep learning-based medical imaging applications. Here we present a transformer-based network for magnetic resonance imaging (MRI) radiology report classification which automates this task by assigning image labels on the basis of free-text expert radiology reports. Our model's performance is comparable to that of an expert radiologist, and better than that of an expert physician, demonstrating the feasibility of this approach. We make code available online for researchers to label the…
Centre for Medical Image Computing, University College London（伦敦大学学院医学图像计算中心）；Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School（马萨诸塞总医院和哈佛医学院马蒂诺斯生物医学成像中心）；Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology（麻省理工学院计算机科学与人工智能实验室）
Partial voluming (PV) is arguably the last crucial unsolved problem in Bayesian segmentation of brain MRI with probabilistic atlases. PV occurs when voxels contain multiple tissue classes, giving rise to image intensities that may not be representative of any one of the underlying classes. PV is particularly problematic for segmentation when there is a large resolution gap between the atlas and the test scan, e.g., when segmenting clinical scans with thick slices, or when using a high-resolution atlas. In this work, we present PV-SynthSeg, a convolutional neural network (CNN) that tackles this…
Thomas Jefferson High School for Science and Technology（托马斯·杰斐逊科技高中）
Glioblastoma Multiforme (GBM) is a malignant brain cancer forming around 48% of al brain and Central Nervous System (CNS) cancers. It is estimated that annually over 13,000 deaths occur in the US due to GBM, making it crucial to have early diagnosis systems that can lead to predictable and effective treatment. The most common treatment after GBM diagnosis is chemotherapy, which works by sending rapidly dividing cells to apoptosis. However, this form of treatment is not effective when the MGMT promoter sequence is methylated, and instead leads to severe side effects decreasing patient survivabi…
