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Machine Learning-Based Reconstruction of 2D MRI for Quantitative Morphometry in Epilepsy 基于机器学习的二维磁共振成像重构,用于癫痫的定量形态测量
Pub Date : 2024-06-24 DOI: 10.1101/2024.06.24.24309298
Corey Ratcliffe, Christophe de Bezenac, Kumar Das, Shubhabrata Biswas, Anthony Marson, Simon S. Keller
Introduction: Structural neuroimaging analyses require 'research quality' images, acquired with costly MRI acquisitions. Isotropic (3D) T1 images are desirable for quantitative analyses, however a routine compromise in the clinical setting is to acquire anisotropic (2D) analogues for qualitative visual inspection. Machine learning-based software have shown promise in addressing some of the limitations of 2D scans in research applications, yet their efficacy in quantitative research is not well understood. To evaluate the applicability of image preprocessing methods, morphometry in idiopathic generalised epilepsy (IGE)--in which, pathology-related abnormalities of the subcortical structures have been reproducibly demonstrated--was investigated first in 3D scans, then in 2D scans, resampled images, and synthesised images. Methods: 2D and 3D T1 MRI were acquired during the same scanning session from 31 individuals (males = 14, mean age = 32.16) undergoing evaluation for IGE at the Walton Centre NHS Foundation Trust, Liverpool, as well as 39 healthy age- and sex-matched controls (males = 16, mean age = 32.13). The DL+DiReCT pipeline was used to provide segmentations of the 2D images, and estimates of regional volume and thickness. The 2D scans were also resampled into isotropic images using NiBabel, and preprocessed into synthetic isotropic images using SynthSR. For the 3D scans, untransformed 2D scans, resampled images, and synthesised images, FreeSurfer 7.2.0 was used to create parcellations of 178 anatomical regions (equivalent to the 178 parcellations provided as part of the DL+DiReCT pipeline), defined by the aseg and Destrieux atlases, and FSL FIRST was used to segment subcortical surface shapes. Spatial correspondence and intraclass correlations between the morphometrics of the five parcellations were first determined, then subcortical surface shape abnormalities associated with IGE were identified by comparing the FSL FIRST outputs of patients with controls. Results: When standardised to the metrics derived from the 3D scans, cortical volume and thickness estimates trended lower for the untransformed 2D, DL+DiReCT, resampled, and SynthSR images, whereas subcortical volume estimates did not differ. Dice coefficients revealed a low spatial similarity between the cortices of the 3D scans and the other images overall, which was higher in the subcortical structures. Intraclass correlation coefficients reiterated this disparity, with estimates of thickness being less similar than those of volume, and DL+DiReCT estimates trending less similar than the other images types. For the people with epilepsy, the 3D scans showed significant surface deflations across various subcortical structures when compared to healthy controls. Analysis of the untransformed 2D scans enabled the detection of a subset of subcortical abnormalities, whereas analyses of the resampled and synthetic images attenuated almost all significance. Conclusions: Generalised image synthe
简介神经影像结构分析需要 "研究质量 "的图像,这些图像需要通过昂贵的磁共振成像采集获得。各向同性(三维)T1 图像是进行定量分析的理想选择,但在临床环境中,常规的折衷方法是获取各向异性(二维)的类似图像进行定性视觉检查。基于机器学习的软件有望解决二维扫描在研究应用中的一些局限性,但它们在定量研究中的功效还不甚了解。为了评估图像预处理方法的适用性,我们首先通过三维扫描,然后通过二维扫描、重采样图像和合成图像对特发性广泛性癫痫(IGE)的形态计量进行了研究。方法:在利物浦沃尔顿中心 NHS 基金会信托公司接受 IGE 评估的 31 人(男性 = 14 人,平均年龄 = 32.16 岁)以及 39 名年龄和性别匹配的健康对照者(男性 = 16 人,平均年龄 = 32.13 岁)在同一扫描时段获得了二维和三维 T1 MRI。DL+DiReCT 管道用于对二维图像进行分割,并估算区域体积和厚度。此外,还使用 NiBabel 将二维扫描图像重新采样为各向同性图像,并使用 SynthSR 将其预处理为合成各向同性图像。对于三维扫描、未转换的二维扫描、重采样图像和合成图像,FreeSurfer 7.2.0 被用来创建由 aseg 和 Destrieux 图集定义的 178 个解剖区域的parcellations(相当于 DL+DiReCT 管道中提供的 178 个parcellations),FSL FIRST 被用来分割皮层下表面形状。首先确定五个旁区形态计量学之间的空间对应性和类内相关性,然后通过比较患者和对照组的 FSL FIRST 输出结果,确定与 IGE 相关的皮层下表面形态异常。结果:与三维扫描得出的指标标准化后,未经转换的二维、DL+DiReCT、重采样和 SynthSR 图像的皮质体积和厚度估计值呈下降趋势,而皮质下体积估计值则没有差异。骰子系数显示,三维扫描的皮层与其他图像的空间相似性总体较低,皮层下结构的相似性更高。类内相关系数重申了这一差异,厚度估计值的相似性低于体积估计值,DL+DiReCT 估计值的相似性趋势低于其他类型的图像。与健康对照组相比,癫痫患者的三维扫描结果显示皮层下各种结构的表面有明显的塌陷。对未转换的二维扫描图像进行分析后,可以检测出皮层下异常的一部分,而对重采样和合成图像进行分析后,几乎所有异常都变得不明显了。结论:通用图像合成方法目前无法减弱各向异性磁共振成像扫描中低通透平面分辨率所导致的部分容积效应,因此使用二维图像进行定量分析时应谨慎解读,研究人员应考虑预处理的潜在影响。关键词:癫痫、定量 MRI、深度学习、图像合成、形态测量、形状分析
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引用次数: 0
RaTEScore: A Metric for Radiology Report Generation RaTEScore:放射学报告生成指标
Pub Date : 2024-06-24 DOI: 10.1101/2024.06.24.24309405
Weike Zhao, Chaoyi Wu, Xiaoman Zhang, Ya Zhang, Yanfeng Wang, Weidi Xie
This paper introduces a novel, entity-aware metric, termed as Radiological Report (Text) Evaluation (RaTEScore), to assess the quality of medical reports generated by AI models. RaTEScore emphasizes crucial medical entities such as diagnostic outcomes and anatomical details, and is robust against complex medical synonyms and sensitive to negation expressions. Technically, we developed a comprehensive medical NER dataset, RaTE-NER, and trained an NER model specifically for this purpose. This model enables the decomposition of complex radiological reports into constituent medical entities. The metric itself is derived by comparing the similarity of entity embeddings, obtained from a language model, based on their types and relevance to clinical significance. Our evaluations demonstrate that RaTEScore aligns more closely with human preference than existing metrics, validated both on established public benchmarks and our newly proposed RaTE-Eval benchmark.
本文介绍了一种新颖的实体感知度量方法,称为放射报告(文本)评估(RaTEScore),用于评估人工智能模型生成的医疗报告的质量。RaTEScore 强调诊断结果和解剖细节等关键医学实体,对复杂的医学同义词具有鲁棒性,对否定表达也很敏感。在技术上,我们开发了一个全面的医学 NER 数据集 RaTE-NER,并专门为此训练了一个 NER 模型。该模型可将复杂的放射报告分解为组成医疗实体。该指标本身是通过比较从语言模型中获得的实体嵌入的相似性而得出的,其依据是实体的类型和与临床意义的相关性。我们的评估结果表明,与现有指标相比,RaTEScore 更符合人类的偏好,这一点在已有的公共基准和我们新提出的 RaTE-Eval 基准上都得到了验证。
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引用次数: 0
Reproducibility of radiomic features of the brain on ultrahigh-resolution MRI at 7 Tesla: a comparison of different segmentation techniques 7 特斯拉超高分辨率磁共振成像脑放射学特征的再现性:不同分割技术的比较
Pub Date : 2024-06-24 DOI: 10.1101/2024.06.24.24308597
Julian Klinger, Doris Leithner, Sungmin Woo, Michael Weber, Hebert Alberto Vargas, Marius E. Mayerhoefer
Objectives: To determine the impact of segmentation techniques on radiomic features extracted from ultrahigh-field (UHF) MRI of the brain. Materials and Methods: Twenty-one 7T MRI scans of the brain, including a 3D magnetization-prepared two rapid acquisition gradient echo (MP2RAGE) T1-weighted sequence with an isotropic 0.63 mm3 voxel size, were analyzed. Radiomic features (histogram, texture, and shape; total n=101) from six brain regions -cerebral gray and white matter, basal ganglia, ventricles, cerebellum, and brainstem- were extracted from segmentation masks constructed with four different techniques: the iGT (reference standard), based on a custom pipeline that combined automatic segmentation tools and expert reader correction; the deep-learning algorithm Cerebrum-7T; the Freesurfer-v7 software suite; and the Nighres algorithm. Principal components (PCs) were calculated for histogram and texture features. To test the reproducibility of radiomic features, intraclass correlation coefficients (ICC) were used to compare Cerebrum-7, Freesurfer-v7, and Nighres to the iGT, respectively. Results: For histogram PCs, median ICCs for Cerebrum-7T, Freesurfer-v7, and Nighres were 0.99, 0.42, and 0.11 for the gray matter; 0.84, 0.25, and 0.43 for the basal ganglia; 0.89, 0.063, and 0.036 for the white matter; 0.84, 0.21, and 0.33 for the ventricles; 0.94, 0.64, and 0.93 for the cerebellum; and 0.78, 0.21, and 0.53 for the brainstem. For texture PCs, median ICCs for Cerebrum-7T, Freesurfer-v7, and Nighres were 0.95, 0.21, and 0.15 for the gray matter; 0.70, 0.36, and 0.023 for the basal ganglia; 0.91, 0.25, and 0.023 for the white matter; 0.80, 0.75, and 0.59 for the ventricles; 0.95, 0.43, and 0.86 for the cerebellum; and 0.72, 0.39, and 0.46 for the brainstem. For shape features, median ICCs for Cerebrum-7T, FreeSurfer-v7, and Nighres were 0.99, 0.91, and 0.36 for the gray matter; 0.89, 0.90, and 0.13 for the basal ganglia; 0.98, 0.91, and 0.027 for the white matter; 0.91, 0.91, and 0.36 for the ventricles; 0.80, 0.68, and 0.47 for the cerebellum; and 0.79, 0.17, and 0.15 for the brainstem. Conclusions: Radiomic features in UHF MRI of the brain show substantial variability depending on the segmentation algorithm. The deep learning algorithm Cerebrum-7T enabled the highest reproducibility. Dedicated software tools for UHF MRI may be needed to achieve more stable results.
目的确定分割技术对从大脑超高场(UHF)磁共振成像中提取的放射学特征的影响。材料与方法:对 21 个 7T 脑部 MRI 扫描进行分析,包括三维磁化预处理双快速采集梯度回波(MP2RAGE)T1 加权序列,各向同性 0.63 mm3 体素大小。从四种不同技术构建的分割掩膜中提取了六个脑区(大脑灰质和白质、基底节、脑室、小脑和脑干)的放射学特征(直方图、纹理和形状;总人数=101):iGT(参考标准),基于结合自动分割工具和专家校正的定制管道;深度学习算法 Cerebrum-7T;Freesurfer-v7 软件套件;以及 Nighres 算法。计算了直方图和纹理特征的主成分(PC)。为了测试放射学特征的可重复性,使用类内相关系数(ICC)将 Cerebrum-7、Freesurfer-v7 和 Nighres 分别与 iGT 进行比较。结果显示对于直方图 PC,Cerebrum-7T、Freesurfer-v7 和 Nighres 的中位 ICC 分别为:灰质 0.99、0.42 和 0.11;基底节 0.84、0.25 和 0.43;基底节 0.白质分别为 0.89、0.063 和 0.036;脑室分别为 0.84、0.21 和 0.33;小脑分别为 0.94、0.64 和 0.93;脑干分别为 0.78、0.21 和 0.53。对于纹理 PC,Cerebrum-7T、Freesurfer-v7 和 Nighres 的中位 ICCs 分别为:灰质 0.95、0.21 和 0.15;基底节 0.70、0.36 和 0.023;脑室 0.91、0.25 和 0.93;小脑 0.94、0.64 和 0.93;脑干 0.78、0.21 和 0.53。91、0.25 和 0.023;脑室为 0.80、0.75 和 0.59;小脑为 0.95、0.43 和 0.86;脑干为 0.72、0.39 和 0.46。在形状特征方面,Cerebrum-7T、FreeSurfer-v7 和 Nighres 的中位 ICC 分别为:灰质 0.99、0.91 和 0.36;基底节 0.89、0.90 和 0.13;脑干 0.98、0.91 和 0.46;脑室 0.95、0.43 和 0.86;小脑 0.72、0.39 和 0.46。98、0.91 和 0.027;脑室为 0.91、0.91 和 0.36;小脑为 0.80、0.68 和 0.47;脑干为 0.79、0.17 和 0.15。结论大脑超高频磁共振成像的放射学特征因分割算法的不同而存在很大差异。深度学习算法 Cerebrum-7T 的可重复性最高。要获得更稳定的结果,可能需要专门的超高频磁共振成像软件工具。
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引用次数: 0
MVP-VSASL: measuring MicroVascular Pulsatility using Velocity-Selective Arterial Spin Labeling MVP-VSASL:利用速度选择性动脉自旋标记测量微血管脉动率
Pub Date : 2024-06-23 DOI: 10.1101/2024.06.21.24309261
Conan Chen, Ryan A Barnes, Katherine J Bangen, Fei Han, Josef Pfeuffer, Eric C Wong, Thomas T Liu, Divya S Bolar
Purpose: By leveraging the small-vessel specificity of velocity-selective arterial spin labeling (VSASL), we present a novel technique for measuring cerebral MicroVascular Pulsatility named MVP-VSASL.Theory and Methods: We present a theoretical model relating the pulsatile, cerebral blood flow-driven VSASL signal to the microvascular pulsatility index (PI), a widely used metric for quantifying cardiac-dependent fluctuations. The model describes the dependence of PI on bolus duration τ (an adjustable VSASL sequence parameter) and provides guidance for selecting a value of τ that maximizes the SNR of the PI measurement. The model predictions were assessed in humans using data acquired with retrospectively cardiac-gated VSASL sequences over a broad range of τ values. In vivo measurements were also used to demonstrate the feasibility of whole-brain voxel-wise PI mapping, assess intrasession repeatability of the PI measurement, and illustrate the potential of this method to explore an association with age.Results: The theoretical model showed excellent agreement to the empirical data in a gray matter region of interest (average R2 value of 0.898 ± 0.107 across six subjects). We further showed excellent intrasession repeatability of the pulsatility measurement (ICC = 0.960, p < 0.001) and the potential to characterize associations with age (r = 0.554, p = 0.021).Conclusion: We have introduced a novel, VSASL-based cerebral microvascular pulsatility technique, which may facilitate investigation of cognitive disorders where damage to the microvasculature has been implicated.
目的:通过利用速度选择性动脉自旋标记(VSASL)的小血管特异性,我们提出了一种测量脑微血管搏动性的新技术,名为 MVP-VSASL:我们提出了一个将脉动性、脑血流驱动的 VSASL 信号与微血管脉动指数(PI)相关联的理论模型,PI 是一种广泛用于量化心脏依赖性波动的指标。该模型描述了搏动指数对栓塞持续时间τ(一个可调节的 VSASL 序列参数)的依赖性,并为选择一个能使搏动指数测量信噪比最大化的 τ 值提供了指导。利用回溯性心脏门控 VSASL 序列在广泛的 τ 值范围内获得的数据,对人体模型预测进行了评估。体内测量还用于证明全脑体素 PI 映射的可行性、评估 PI 测量的会期内可重复性,并说明该方法探索与年龄相关性的潜力:理论模型与灰质相关区域的经验数据显示出极佳的一致性(六个受试者的平均 R2 值为 0.898 ± 0.107)。我们还进一步证明了脉动性测量的极佳时段内可重复性(ICC = 0.960,p < 0.001)以及与年龄相关的潜在特征(r = 0.554,p = 0.021):我们介绍了一种基于 VSASL 的新型脑微血管搏动率技术,该技术可能有助于对微血管受损的认知障碍进行研究。
{"title":"MVP-VSASL: measuring MicroVascular Pulsatility using Velocity-Selective Arterial Spin Labeling","authors":"Conan Chen, Ryan A Barnes, Katherine J Bangen, Fei Han, Josef Pfeuffer, Eric C Wong, Thomas T Liu, Divya S Bolar","doi":"10.1101/2024.06.21.24309261","DOIUrl":"https://doi.org/10.1101/2024.06.21.24309261","url":null,"abstract":"<strong>Purpose:</strong> By leveraging the small-vessel specificity of velocity-selective arterial spin labeling (VSASL), we present a novel technique for measuring cerebral MicroVascular Pulsatility named MVP-VSASL.\u0000<strong>Theory and Methods:</strong> We present a theoretical model relating the pulsatile, cerebral blood flow-driven VSASL signal to the microvascular pulsatility index (PI), a widely used metric for quantifying cardiac-dependent fluctuations. The model describes the dependence of PI on bolus duration τ (an adjustable VSASL sequence parameter) and provides guidance for selecting a value of τ that maximizes the SNR of the PI measurement. The model predictions were assessed in humans using data acquired with retrospectively cardiac-gated VSASL sequences over a broad range of τ values. In vivo measurements were also used to demonstrate the feasibility of whole-brain voxel-wise PI mapping, assess intrasession repeatability of the PI measurement, and illustrate the potential of this method to explore an association with age.\u0000<strong>Results:</strong> The theoretical model showed excellent agreement to the empirical data in a gray matter region of interest (average R<sup>2</sup> value of 0.898 ± 0.107 across six subjects). We further showed excellent intrasession repeatability of the pulsatility measurement (ICC = 0.960, p &lt; 0.001) and the potential to characterize associations with age (r = 0.554, p = 0.021).\u0000<strong>Conclusion:</strong> We have introduced a novel, VSASL-based cerebral microvascular pulsatility technique, which may facilitate investigation of cognitive disorders where damage to the microvasculature has been implicated.","PeriodicalId":501358,"journal":{"name":"medRxiv - Radiology and Imaging","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141503297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mammographic density assessed using deep learning in women at high risk of developing breast cancer: the effect of weight change on density 利用深度学习评估乳腺癌高危妇女的乳腺密度:体重变化对密度的影响
Pub Date : 2024-06-23 DOI: 10.1101/2024.06.22.24309234
Steven Squires, Michelle Harvie, Anthony Howell, D Gareth Evans, Susan M Astley
Objectives: High mammographic density (MD) and excess weight are associated with increased risk of breast cancer. Weight loss interventions could reduce risk, but classically defined percentage density measures may not reflect this due to disproportionate loss of breast fat. We investigate an artificial intelligence-based density method, reporting density changes in 46 women enrolled in a weight-loss study in a family history breast cancer clinic, using a volumetric density method as a comparison. Methods: We analysed data from women who had weight recorded and mammograms taken at the start and end of the 12-month weight intervention study. MD was assessed at both time points using a deep learning model, pVAS, trained on expert estimates of percent density, and VolparaTM density software. Results: The Spearman rank correlation between reduction in weight and change in density was 0.17 (-0.13 to 0.43) for pVAS and 0.59 (0.36 to 0.75) for Volpara volumetric percent density. Conclusions: pVAS percent density measurements were not significantly affected by change in weight. Percent density measured with Volpara increased as weight decreased, driven by changes in fat volume. Advances in knowledge: The effect of weight change on pVAS mammographic density predictions has not previously been published.
目的:乳腺 X 线照相密度(MD)高和体重超重与乳腺癌风险增加有关。减肥干预措施可以降低风险,但由于乳房脂肪的不成比例损失,经典定义的百分比密度测量可能无法反映这一点。我们研究了一种基于人工智能的密度方法,报告了在家族史乳腺癌诊所参加减肥研究的 46 名妇女的密度变化,并使用体积密度方法作为对比。研究方法我们分析了在为期 12 个月的体重干预研究开始和结束时记录体重和进行乳房 X 光检查的妇女的数据。使用深度学习模型 pVAS 和 VolparaTM 密度软件对两个时间点的 MD 进行评估。结果显示体重下降与密度变化之间的斯皮尔曼等级相关性为:pVAS 为 0.17(-0.13 至 0.43),Volpara 容积百分比密度为 0.59(0.36 至 0.75)。结论:体重变化对 pVAS 百分密度测定的影响不大。Volpara 测量的百分比密度随着体重的下降而增加,这是脂肪体积变化的结果。知识进步:体重变化对 pVAS 乳房 X 线照相术密度预测的影响以前从未发表过。
{"title":"Mammographic density assessed using deep learning in women at high risk of developing breast cancer: the effect of weight change on density","authors":"Steven Squires, Michelle Harvie, Anthony Howell, D Gareth Evans, Susan M Astley","doi":"10.1101/2024.06.22.24309234","DOIUrl":"https://doi.org/10.1101/2024.06.22.24309234","url":null,"abstract":"Objectives: High mammographic density (MD) and excess weight are associated with increased risk of breast cancer. Weight loss interventions could reduce risk, but classically defined percentage density measures may not reflect this due to disproportionate loss of breast fat. We investigate an artificial intelligence-based density method, reporting density changes in 46 women enrolled in a weight-loss study in a family history breast cancer clinic, using a volumetric density method as a comparison. Methods: We analysed data from women who had weight recorded and mammograms taken at the start and end of the 12-month weight intervention study. MD was assessed at both time points using a deep learning model, pVAS, trained on expert estimates of percent density, and VolparaTM density software. Results: The Spearman rank correlation between reduction in weight and change in density was 0.17 (-0.13 to 0.43) for pVAS and 0.59 (0.36 to 0.75) for Volpara volumetric percent density. Conclusions: pVAS percent density measurements were not significantly affected by change in weight. Percent density measured with Volpara increased as weight decreased, driven by changes in fat volume. Advances in knowledge: The effect of weight change on pVAS mammographic density predictions has not previously been published.","PeriodicalId":501358,"journal":{"name":"medRxiv - Radiology and Imaging","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141503298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Systematic Review of Hybrid Vision Transformer Architectures for Radiological Image Analysis 用于放射图像分析的混合视觉变换器架构系统综述
Pub Date : 2024-06-22 DOI: 10.1101/2024.06.21.24309265
Ji Woong Kim, Aisha Urooj Khan, Imon Banerjee
Background: Vision Transformer (ViT) and Convolutional Neural Networks (CNNs) each possess distinct strengths in medical imaging: ViT excels in capturing long-range dependencies through self-attention, while CNNs are adept at extracting local features via spatial convolution filters. While ViTs might struggle with capturing detailed local spatial information critical for tasks like anomaly detection in medical imaging, shallow CNNs often fail to effectively abstract global context.Objective: This study aims to explore and evaluate hybrid architectures that integrate ViT and CNN to lever- age their complementary strengths for enhanced performance in medical vision tasks, such as segmentation, classification, and prediction.Methods: Following PRISMA guideline, a systematic review was conducted on 28 articles published between 2020 and 2023. These articles proposed hybrid ViT-CNN architectures specifically for medical imaging tasks in radiology. The review focused on analyzing architectural variations, merging strategies between ViT and CNN, innovative applications of ViT, and efficiency metrics including parameters, inference time (GFlops), and performance benchmarks.Results: The review identified that integrating ViT and CNN can help mitigate the limitations of each architecture, offering comprehensive solutions that combine global context understanding with precise local feature extraction. We benchmarked the articles based on architectural variations, merging strategies, innovative uses of ViT, and efficiency metrics (number of parameters, inference time (GFlops), performance).Conclusion: By synthesizing current literature, this review defines fundamental concepts of hybrid vision transformers and highlights emerging trends in the field. It provides a clear direction for future research aimed at optimizing the integration of ViT and CNN for effective utilization in medical imaging, contributing to advancements in diagnostic accuracy and image analysis.
背景:视觉转换器(ViT)和卷积神经网络(CNN)在医学成像方面各有所长:ViT 擅长通过自我关注捕捉长距离依赖关系,而 CNN 则擅长通过空间卷积滤波器提取局部特征。ViT 可能难以捕捉对医学成像中异常检测等任务至关重要的详细局部空间信息,而浅层 CNN 则往往无法有效抽象出全局上下文:本研究旨在探索和评估整合了 ViT 和 CNN 的混合架构,利用它们的互补优势来提高医疗视觉任务(如分割、分类和预测)的性能:按照 PRISMA 准则,对 2020 年至 2023 年间发表的 28 篇文章进行了系统性综述。这些文章专门针对放射学中的医学成像任务提出了混合 ViT-CNN 架构。综述重点分析了架构的变化、ViT 与 CNN 的合并策略、ViT 的创新应用以及效率指标,包括参数、推理时间(GFlops)和性能基准:综述发现,整合 ViT 和 CNN 有助于缓解每种架构的局限性,提供结合全局上下文理解和精确局部特征提取的全面解决方案。我们根据架构变化、合并策略、ViT 的创新应用以及效率指标(参数数量、推理时间(GFlops)、性能)对文章进行了基准测试:本综述综合了当前的文献,定义了混合视觉转换器的基本概念,并强调了该领域的新兴趋势。它为未来的研究提供了明确的方向,旨在优化 ViT 和 CNN 的集成,以便在医学成像中有效利用,从而促进诊断准确性和图像分析的进步。
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引用次数: 0
Quantitative sodium-MRI detects differential sodium content in benign vs. malignant oncocytic renal tumours 定量钠-MRI 检测良性与恶性肿瘤性肾肿瘤中不同的钠含量
Pub Date : 2024-06-20 DOI: 10.1101/2024.06.19.24309026
Ines Horvat-Menih, Jonathan R Birchall, Maria J Zamora-Morales, Alice Bebb, Joshua Kaggie, Frank Riemer, Andrew B Gill, Andrew N Priest, Marta Wylot, Iosif A Mendichovszky, Anne Y Warren, James O Jones, James N Armitage, Thomas J Mitchell, Grant D Stewart, Mary A McLean, Ferdia A Gallagher
Background: Accurate non-invasive subtyping of localised kidney tumours is an unmet clinical question in uro-oncology. Differentiation of benign renal oncocytomas (RO) from malignant chromophobe renal cell carcinomas (chRCC) is not possible using conventional imaging. Despite the importance of renal function for sodium regulation, little is known about sodium handling in kidney tumours. Purpose: Here we used non-invasive sodium MRI (23Na-MRI) to quantify sodium concentration and relaxation dynamics across a range of different kidney tumour subtypes and have correlated these findings with imaging surrogates for perfusion, hypoxia, and cellularity. Materials and Methods: Between January and April 2023, patients with localised renal masses were prospectively recruited and underwent 23Na and proton (1H) MRI at 3T to acquire 3D maps of B1, total sodium concentration (TSC), proton and sodium relaxation rates (R2*), and diffusion weighted imaging (DWI). Statistical analysis included comparison and correlation of quantified imaging parameters across kidney tumour subtypes. Results: Ten patients were included in the final analysis (mean age ± S.D. = 64 ± 8 years; 7:3 male:female ratio) encompassing seven ROs, two chRCCs, two clear cell RCCs (ccRCC), and one papillary RCC (pRCC). The TSC was significantly higher in the ROs compared to the chRCCs: 162 ± 58 mM vs. 71 ± 2 mM (P < 0.05). The mean TSC in ccRCC was 135 ± 59 mM, and 81 mM in pRCC. The 23Na-derived and 1H-derived R2* values showed a weak correlation (Spearman r = 0.17; P = 0.50). There was a significant inverse correlation between TSC and 1H-R2* (Spearman r = -0.39, P < 0.05), but TSC was independent of the DWI-derived imaging parameters. Conclusion: 23Na-MRI detected markedly different sodium concentrations within benign ROs and malignant chRCCs. In addition, the sodium signal inversely correlated with 1H-R2* as a surrogate for hypoxia. Therefore we have shown the feasibility and potential of 23Na-MRI for future research in renal tumours.
背景:对局部肾脏肿瘤进行准确的非侵入性亚型鉴定是泌尿肿瘤学尚未解决的临床问题。良性肾肿瘤细胞瘤(RO)与恶性嗜色性肾细胞癌(chRCC)的鉴别无法通过传统成像技术实现。尽管肾功能对钠的调节非常重要,但人们对肾肿瘤中钠的处理却知之甚少。目的:在此,我们使用无创钠核磁共振成像(23Na-MRI)来量化一系列不同肾脏肿瘤亚型的钠浓度和弛豫动态,并将这些发现与灌注、缺氧和细胞性的成像替代物相关联。材料和方法:在 2023 年 1 月至 4 月期间,前瞻性地招募了局部肾肿块患者,并在 3T 下进行了 23Na 和质子(1H)磁共振成像,以获取 B1、总钠浓度 (TSC)、质子和钠弛豫率 (R2*) 以及弥散加权成像 (DWI) 的三维图。统计分析包括不同肾脏肿瘤亚型的量化成像参数的比较和相关性。结果:最终分析包括10名患者(平均年龄±S.D. = 64 ± 8岁;男女比例为7:3),其中包括7例RO、2例chRCC、2例透明细胞RCC(ccRCC)和1例乳头状RCC(pRCC)。与chRCC相比,RO的TSC明显更高:162 ± 58 mM vs. 71 ± 2 mM(P <0.05)。ccRCC的平均TSC为135 ± 59 mM,pRCC为81 mM。23Na 导出的 R2* 值和 1H 导出的 R2* 值显示出微弱的相关性(Spearman r = 0.17;P = 0.50)。TSC与1H-R2*之间存在明显的反相关性(Spearman r = -0.39,P <0.05),但TSC与DWI衍生成像参数无关。结论:23Na-MRI 在良性 RO 和恶性 chRCC 中检测到明显不同的钠浓度。此外,钠信号与作为缺氧代用指标的 1H-R2* 呈反相关。因此,我们证明了 23Na-MRI 在未来肾肿瘤研究中的可行性和潜力。
{"title":"Quantitative sodium-MRI detects differential sodium content in benign vs. malignant oncocytic renal tumours","authors":"Ines Horvat-Menih, Jonathan R Birchall, Maria J Zamora-Morales, Alice Bebb, Joshua Kaggie, Frank Riemer, Andrew B Gill, Andrew N Priest, Marta Wylot, Iosif A Mendichovszky, Anne Y Warren, James O Jones, James N Armitage, Thomas J Mitchell, Grant D Stewart, Mary A McLean, Ferdia A Gallagher","doi":"10.1101/2024.06.19.24309026","DOIUrl":"https://doi.org/10.1101/2024.06.19.24309026","url":null,"abstract":"Background: Accurate non-invasive subtyping of localised kidney tumours is an unmet clinical question in uro-oncology. Differentiation of benign renal oncocytomas (RO) from malignant chromophobe renal cell carcinomas (chRCC) is not possible using conventional imaging. Despite the importance of renal function for sodium regulation, little is known about sodium handling in kidney tumours. Purpose: Here we used non-invasive sodium MRI (23Na-MRI) to quantify sodium concentration and relaxation dynamics across a range of different kidney tumour subtypes and have correlated these findings with imaging surrogates for perfusion, hypoxia, and cellularity. Materials and Methods: Between January and April 2023, patients with localised renal masses were prospectively recruited and underwent 23Na and proton (1H) MRI at 3T to acquire 3D maps of B1, total sodium concentration (TSC), proton and sodium relaxation rates (R2*), and diffusion weighted imaging (DWI). Statistical analysis included comparison and correlation of quantified imaging parameters across kidney tumour subtypes. Results: Ten patients were included in the final analysis (mean age ± S.D. = 64 ± 8 years; 7:3 male:female ratio) encompassing seven ROs, two chRCCs, two clear cell RCCs (ccRCC), and one papillary RCC (pRCC). The TSC was significantly higher in the ROs compared to the chRCCs: 162 ± 58 mM vs. 71 ± 2 mM (P &lt; 0.05). The mean TSC in ccRCC was 135 ± 59 mM, and 81 mM in pRCC. The 23Na-derived and 1H-derived R2* values showed a weak correlation (Spearman r = 0.17; P = 0.50). There was a significant inverse correlation between TSC and 1H-R2* (Spearman r = -0.39, P &lt; 0.05), but TSC was independent of the DWI-derived imaging parameters. Conclusion: 23Na-MRI detected markedly different sodium concentrations within benign ROs and malignant chRCCs. In addition, the sodium signal inversely correlated with 1H-R2* as a surrogate for hypoxia. Therefore we have shown the feasibility and potential of 23Na-MRI for future research in renal tumours.","PeriodicalId":501358,"journal":{"name":"medRxiv - Radiology and Imaging","volume":"31 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141503300","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mapping Structural Disconnection and Morphometric Similarity Alterations in Multiple Sclerosis 绘制多发性硬化症的结构断裂和形态相似性改变图谱
Pub Date : 2024-06-20 DOI: 10.1101/2024.06.19.24309154
Mario Tranfa, Maria Petracca, Marcello Moccia, Alessandra Scaravilli, Frederik Barkhof, Vincenzo Brescia Morra, Antonio Carotenuto, Sara Collorone, Andrea Elefante, Fabrizia Falco, Roberta Lanzillo, Luigi Lorenzini, Menno Schoonheim, Ahmed Toosy, Arturo Brunetti, Sirio Cocozza, Mario Quarantelli, Giuseppe Pontillo
Whilst multiple sclerosis (MS) can be conceptualized as a network disorder, brain network analyses are typically dependent on advanced MRI sequences not commonly acquired in clinical practice. Here, we used conventional MRI to assess cross-sectional and longitudinal modifications of structural disconnection and morphometric similarity networks in people with MS (pwMS), along with their relationship with clinical disability.In this longitudinal monocentric study, 3T structural MRI scans of pwMS and healthy controls (HC) were retrospectively analysed. Physical and cognitive disabilities were assessed with the expanded disability status scale (EDSS) and the symbol digit modalities test (SDMT), respectively. Demyelinating lesions were automatically segmented on 3D-T1w and FLAIR images and, based on normative tractography data, the corresponding masks were used to compute pairwise structural disconnection between atlas-defined brain regions (100 cortical and 14 subcortical). Using the Morphometric Inverse Divergence (MIND) method, we built matrices of morphometric similarity between cortical regions based on FreeSurfer surface reconstruction. Using network-based statistics (NBS) and its prediction-based extension NBS-predict, we tested whether subject-level connectomes were associated with disease status, progression, clinical disability, and long-term confirmed disability progression (CDP), independently from global lesion burden and atrophy. The coupling between structural disconnection and morphometric similarity was assessed at different scales.We studied 461 pwMS (age=37.2±10.6 years, F/M=324/137), corresponding to 1235 visits (mean follow-up time=1.9±2.0 years, range=0.1-13.3 years), and 55 HC (age=42.4±15.7 years; F/M=25/30). Long-term clinical follow-up was available for 285 pwMS (mean follow-up time=12.4±2.8 years), 127 of whom (44.6%) exhibited CDP. At baseline, structural disconnection in pwMS was mostly centered around the thalami and cortical sensory and association hubs, while morphometric similarity was extensively disrupted (pFWE<0.01). EDSS was related to fronto-thalamic disconnection (pFWE<0.01) and disrupted morphometric similarity around the left perisylvian cortex (pFWE=0.02), whilst SDMT was associated with cortico-subcortical disconnection in the left hemisphere (pFWE<0.01). Longitudinally, both structural disconnection and morphometric similarity disruption significantly progressed (pFWE=0.04 and pFWE<0.01), correlating with EDSS increase (rho=0.07, p=0.02 and rho=0.11, p<0.001), whilst baseline disconnection predicted long-term CDP with nearly 60% accuracy (p=0.03). On average, structural disconnection and morphometric similarity were positively associated at both the edge (rho=0.18, p<0.001) and node (rho=0.16, p<0.001) levels.Structural disconnection and morphometric similarity networks, as assessed through conventional MRI, are sensitive to MS-related brain damage and its progression. They explain di
虽然多发性硬化症(MS)可被视为一种网络障碍性疾病,但大脑网络分析通常依赖于临床实践中并不常见的高级核磁共振成像序列。在这项纵向单中心研究中,我们对多发性硬化症患者和健康对照组(HC)的 3T 结构 MRI 扫描进行了回顾性分析。肢体残疾和认知残疾分别通过扩大残疾状况量表(EDSS)和符号数字模型测试(SDMT)进行评估。脱髓鞘病变在三维-T1w和FLAIR图像上被自动分割,并根据常模牵引成像数据,使用相应的掩膜计算图谱定义的脑区(100个皮层和14个皮层下)之间的成对结构断开。使用形态计量反向发散(MIND)方法,我们根据 FreeSurfer 表面重建建立了皮层区域之间的形态计量相似性矩阵。利用基于网络的统计(NBS)及其基于预测的扩展 NBS-predict,我们测试了受试者水平的连通组是否与疾病状态、进展、临床残疾和长期确诊残疾进展(CDP)相关,而与整体病变负担和萎缩无关。我们研究了 461 名 pwMS(年龄=37.2±10.6 岁,F/M=324/137),对应 1235 次就诊(平均随访时间=1.9±2.0 年,范围=0.1-13.3 年),以及 55 名 HC(年龄=42.4±15.7 岁;F/M=25/30)。对 285 名 pwMS(平均随访时间=12.4±2.8 年)进行了长期临床随访,其中 127 人(44.6%)表现出 CDP。基线时,pwMS 的结构断裂主要集中在丘脑和皮层感觉与联想中枢,而形态相似性则受到广泛破坏(pFWE<0.01)。EDSS与前脑-丘脑断联(pFWE<0.01)和左侧边缘皮层周围的形态计量相似性破坏(pFWE=0.02)有关,而SDMT与左半球皮层-皮层下断联有关(pFWE<0.01)。纵向来看,结构性断裂和形态计量学相似性破坏均显著增加(pFWE=0.04 和 pFWE<0.01),与 EDSS 的增加相关(rho=0.07,p=0.02 和 rho=0.11,p<0.001),而基线断裂预测长期 CDP 的准确率接近 60%(p=0.03)。平均而言,结构断开和形态测量相似性在边缘(rho=0.18,p<0.001)和节点(rho=0.16,p<0.001)水平均呈正相关。它们能解释与疾病相关的临床残疾,并能预测其长期演变,而不受整体病变负荷和萎缩的影响,有可能作为基于网络的疾病严重程度和进展的生物标志物,补充已建立的磁共振成像测量方法。
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引用次数: 0
Cross-Modality Synthetic Data Augmentation using GANs: Enhancing Brain MRI and Chest X-ray Classification 使用 GANs 进行跨模态合成数据增强:增强脑磁共振成像和胸部 X 射线分类
Pub Date : 2024-06-10 DOI: 10.1101/2024.06.09.24308649
KUNAAL DHAWAN, Siddharth S. Nijhawan
Brain MRI scans and chest X-ray imaging are pivotal in diagnosing and managing neurological and respiratory diseases, respectively. Given their importance in diagnosis, the datasets to train the artificial intelligence (AI) models for automated diagnosis remain scarce. As an example, annotated chest X-ray datasets, especially those containing rare or abnormal cases like bacterial pneumonia, are scarce. Conventional dataset collection methods are labor-intensive and costly, exacerbating the data scarcity issue. To overcome these challenges, we propose a specialized Generative Adversarial Network (GAN) architecture for generating synthetic chest X-ray data representing healthy lungs and various pneumonia conditions, including viral and bacterial pneumonia. Additionally, we extended our experiments to brain MRI scans by simply swapping the training dataset and demonstrating the power of our GAN approach across different medical imaging contexts. Our method aims to streamline data collection and labeling processes while addressing privacy concerns associated with patient data. We demonstrate the effectiveness of synthetic data in facilitating the development and evaluation of machine learning algorithms, particularly leveraging an EfficientNet v2 model. Through comprehensive experimentation, we evaluate our approach on both real and synthetic datasets, showcasing the potential of synthetic data augmentation in improving disease classification accuracy across diverse pathological conditions. Indeed, the classifier performance when trained with fake + real data on brain MRI classification task shows highest accuracy at 85.9%. Our findings underscore the promising role of synthetic data in advancing automated diagnosis and treatment planning for pneumonia, other respiratory conditions, and brain pathologies.
脑磁共振成像扫描和胸部 X 射线成像分别是诊断和管理神经系统疾病和呼吸系统疾病的关键。鉴于它们在诊断中的重要性,用于训练自动诊断人工智能(AI)模型的数据集仍然稀缺。举例来说,带注释的胸部 X 光数据集,尤其是包含细菌性肺炎等罕见或异常病例的数据集非常稀缺。传统的数据集收集方法劳动密集且成本高昂,加剧了数据稀缺问题。为了克服这些挑战,我们提出了一种专门的生成对抗网络(GAN)架构,用于生成代表健康肺部和各种肺炎病症(包括病毒性和细菌性肺炎)的合成胸部 X 光数据。此外,我们通过简单地交换训练数据集,将实验扩展到了脑部核磁共振成像扫描,并展示了我们的 GAN 方法在不同医学成像环境下的强大功能。我们的方法旨在简化数据收集和标记过程,同时解决与患者数据相关的隐私问题。我们展示了合成数据在促进机器学习算法的开发和评估方面的有效性,特别是利用 EfficientNet v2 模型。通过全面的实验,我们在真实数据集和合成数据集上评估了我们的方法,展示了合成数据增强在提高不同病理条件下疾病分类准确性方面的潜力。事实上,在脑核磁共振成像分类任务中,使用虚假数据和真实数据训练的分类器准确率最高,达到 85.9%。我们的研究结果凸显了合成数据在推进肺炎、其他呼吸系统疾病和脑部病变的自动诊断和治疗规划方面的巨大潜力。
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引用次数: 0
Prediction of oncogene mutation status in non-small cell lung cancer: A systematic review and meta-analysis with a special focus on artificial-intelligence-based methods 预测非小细胞肺癌的癌基因突变状态:系统综述和荟萃分析,特别关注基于人工智能的方法
Pub Date : 2024-05-31 DOI: 10.1101/2024.05.31.24308261
Almudena Fuster-Matanzo, Alfonso Picó Peris, Fuensanta Bellvís Bataller, Ana Jimenez-Pastor, Glen J. Weiss, Luis Martí-Bonmatí, Antonio Lázaro Sánchez, Giuseppe L. Banna, Alfredo Addeo, Ángel Alberich-Bayarri
Background In non-small cell lung cancer (NSCLC), alternative strategies to determine patient oncogene mutation status are essential to overcome some of the drawbacks associated with current methods. We aimed to review the use of radiomics alone or in combination with clinical data and to evaluate the performance of artificial intelligence (AI)-based models on the prediction of oncogene mutation status.
背景 在非小细胞肺癌(NSCLC)中,确定患者癌基因突变状态的替代策略对于克服现有方法的一些弊端至关重要。我们旨在回顾放射组学单独使用或与临床数据结合使用的情况,并评估基于人工智能(AI)的模型在预测癌基因突变状态方面的性能。
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引用次数: 0
期刊
medRxiv - Radiology and Imaging
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