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  • MRQy quality measures for TCIA MRI datasets (MRQy-Quality-Measures)

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Excerpt

These quality assessment measures were generated for 

  1. T1-weighted post-contrast axial MRI sequences from 133 TCGA-GBM subjects 
  2. T1-weighted post-contrast axial MRI sequences from 46 CPTAC-GBM subjects  
  3. Both T1- and T2-weighted axial MRI sequences from 54 TCGA-CESC subjects

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: http://github.com/ccipd/MRQy.  Manifest files to download the DICOM images these results were derived from are available on the Detailed Description page.

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(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).

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