MRQy quality measures for TCIA MRI datasets

Magnetic Resonance Imaging (MRI) quality assessment measures were generated for<ol><li>T1-weighted post-contrast axial MRI sequences from 133 <a href="/collection/tcga-gbm/" target="_blank" rel="noopener">TCGA-GBM</a> subjects</li><li>T1-weighted post-contrast axial MRI sequences from 46 <a href="/collection/cptac-gbm/" target="_blank" rel="noopener">CPTAC-GBM</a> subjects</li><li>Both T1- and T2-weighted axial MRI sequences from 54 <a href="/collection/tcga-cesc/" target="_blank" rel="noopener">TCGA-CESC</a> subjects</li></ol>All MRI scans for each cohort were downloaded as DICOM files from TCIA and then processed via MRQy to compute quality measures for (a) interrogating the presence of site- or equipment-specific variations within a cohort, and (b) quantifying the impact of MRI artifacts to determine what pre-analytical corrections are needed. The MRQy output can be easily interrogated via the associated HTML5 based front-end, allowing for real-time filtering and visualization. MRQy is available for download at: <a href="http://github.com/ccipd/MRQy">http://github.com/ccipd/MRQy</a>.  Manifest files to download the DICOM images these results were derived from are available in the "Collections Used In This Analysis Result" table.In the figure, see (a) MRQy front-end interface for interrogating TCGA-GBM cohort. (b) Outlier dataset identified on the parallel coordinate chart for the CJV quality measure found to exhibit shading artifacts on (c) representative images, especially when compared to (d) a different dataset without this artifact. (e) t-SNE scatter plot of quality measures revealing presence of site-specific batch effects (colors correspond to different sites, note presence of site-specific clusters).

针对133名TCGA-GBM受试者和46名CPTAC-GBM受试者的T1加权对比增强轴位MRI序列，以及54名TCGA-CESC受试者的T1和T2加权轴位MRI序列，本研究生成了磁共振成像（MRI）质量评估指标。所有队列的MRI扫描均从TCIA下载为DICOM文件，并经过MRQy处理以计算质量指标，旨在（a）探究队列内部是否存在与特定位置或设备相关的差异，以及（b）量化MRI伪影的影响，以确定所需的预处理校正措施。MRQy的输出可通过基于HTML5的前端界面轻松查询，实现实时过滤和可视化。MRQy可在以下链接下载：http://github.com/ccipd/MRQy。此外，用于下载这些结果所依据的DICOM图像的清单文件可在“在此分析结果中使用的集合”表中找到。在图中，（a）展示了用于查询TCGA-GBM队列的MRQy前端界面。（b）在并行坐标图上识别出的异常数据集，该数据集在（c）代表性图像上表现出阴影伪影，尤其是在与（d）未出现此伪影的另一个数据集进行比较时。（e）质量指标的t-SNE散点图揭示了存在与特定位置相关的批次效应，颜色对应不同的位置，请注意存在与特定位置相关的聚类。