论文标题

SKM-TEA:具有密集图像标签的加速MRI重建数据集用于定量临床评估

SKM-TEA: A Dataset for Accelerated MRI Reconstruction with Dense Image Labels for Quantitative Clinical Evaluation

论文作者

Desai, Arjun D, Schmidt, Andrew M, Rubin, Elka B, Sandino, Christopher M, Black, Marianne S, Mazzoli, Valentina, Stevens, Kathryn J, Boutin, Robert, Ré, Christopher, Gold, Garry E, Hargreaves, Brian A, Chaudhari, Akshay S

论文摘要

磁共振成像(MRI)是现代医学成像的基石。然而,较长的图像获取时间,对定性专家分析的需求以及对组织健康敏感的定量指标缺乏(且难以提取)的定量指标减少了广泛的临床和研究。尽管最近用于MRI重建和分析的机器学习方法显示了减轻这种负担的希望,但这些技术主要通过不完美的图像质量指标来验证,这些指标与临床上与临床相关的措施不符,最终阻碍了临床部署和临床医生的信任。为了减轻这一挑战,我们通过多任务评估(SKM-TEA)数据集介绍了斯坦福膝关节MRI,这是一个定量膝关节MRI(QMRI)扫描的集合,可实现对MRI重建和分析工具的端到端,临床上相关的评估。该1.6TB数据集由约25,000张(155例)匿名患者MRI扫描的原始数据测量,相应的扫描仪生成的DICOM图像,四个组织的手动分割以及16个临床相关的病理学的边界盒注释。我们提供了使用QMRI参数图以及图像重建和致密图像标签的框架,用于测量从MRI重建,分割和检测技术中提取的QMRI生物标志物估计的质量。最后,我们使用此框架来基于此数据集的最新基线。我们希望我们的SKM-TEA数据集和代码能够以临床知情的方式为模块化图像重建和图像分析提供广泛的研究。数据集访问,代码和基准可在https://github.com/stanfordmimi/skm-tea上找到。

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.

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