SummaryMagnetic Resonance Imaging (MRI) quality assessment measures were generated for
- T1-weighted post-contrast axial MRI sequences from 133 TCGA-GBM subjects
- T1-weighted post-contrast axial MRI sequences from 46 CPTAC-GBM subjects
- 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.
(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).
Research reported in this publication was supported by:
- National Cancer Institute of the National Institutes of Health under award numbers 1U24CA199374-01, R01CA202752-01A1, R01CA208236-01A1, R01 CA216579-01A1, R01 CA220581-01A1, 1U01 CA239055-01, 1F31CA216935-01A1, NCI 1U01CA248226-01
- National Institute for Biomedical Imaging and Bioengineering (1R43EB028736-01)
- National Center for Research Resources under award number 1 C06 RR12463-01
- VA Merit Review Award IBX004121A from the United States Department of Veterans Affairs Biomedical Laboratory Research and Development Service
- The DoD Breast Cancer Research Program Breakthrough Level 1 Award (W81XWH-19-1-0668)
- The DOD Prostate Cancer Idea Development Award (W81XWH-15-1-0558)
- The DOD Lung Cancer Investigator-Initiated Translational Research Award (W81XWH-18-1-0440)
- The DOD Peer Reviewed Cancer Research Program (W81XWH-16-1-0329, W81XWH-18-1-0404)
- Dana Foundation David Mahoney Neuroimaging Program
- The V Foundation Translational Research Award
- The Ohio Third Frontier Technology Validation Fund
- The Wallace H. Coulter Foundation Program in the Department of Biomedical Engineering
- The Clinical and Translational Science Award Program (CTSA) at Case Western Reserve University
|Data Type||Download all or Query/Filter|
|TCGA-GBM MRQy results (XLS)|
|TCGA-CESC MRQy results (XLS)|
|CPTAC-GBM MRQy results (XLS)|
Corresponding Original MR Images from TCGA-GBM (DICOM, 1.37GB)
Corresponding Original MR Images from CPTAC-GBM (DICOM, 0.4 GB)
Corresponding Original MR Images from TCGA-CESC subjects (DICOM, 2.72 GB)
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Collections Used in this Third Party Analysis
Below is a list of the Collections used in these analyses:
The spreadsheets provided are derived analyses from subsets of images from the TCGA-GBM, CPTAC-GBM, and TCGA-CESC collections. To download the corresponding images for your own analysis you can use the table below:
|Data Type||Download all or Query/Filter|
|TCGA-GBM MRQy Images (DICOM)|
|TCGA-CESC MRQy Images (DICOM)|
|CPTAC-GBM MRQy Images (DICOM)|
Please be sure to cite each Collection you use according to the Citations & Data Usage policy outlined on each Collection's page. If you have any questions or issues, please contact email@example.com.
Citations & Data Usage Policy
Users of this data must abide by the TCIA Data Usage Policy and the Creative Commons Attribution 3.0 Unported License under which it has been published. Attribution should include references to the following citations:
Sadri, A. R., Janowczyk, A., Verma, R., Antunes, J., Madabhushi, A., Tiwari, P., & Viswanath, S. (2020). MRQy quality measures for TCIA MRI datasets [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2020.JHZ2-T694
Clark, K., Vendt, B., Smith, K., Freymann, J., Kirby, J., Koppel, P., Moore, S., Phillips, S., Maffitt, D., Pringle, M., Tarbox, L., & Prior, F. (2013). The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository. Journal of Digital Imaging, 26(6), 1045–1057. https://doi.org/10.1007/s10278-013-9622-7