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

Summary

Magnetic Resonance Imaging (MRI) quality assessment measures were generated for

T1-weighted post-contrast axial MRI sequences from 133 The Cancer Genome Atlas Glioblastoma Multiforme Collection (TCGA-GBM) subjects
T1-weighted post-contrast axial MRI sequences from 46 The Clinical Proteomic Tumor Analysis Consortium Glioblastoma Multiforme Collection (CPTAC-GBM) subjects
Both T1- and T2-weighted axial MRI sequences from 54 The Cancer Genome Atlas Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma Collection (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.

Acknowledgements

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

(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).

Data Access

Data Type	Download all or Query/Filter	License
TCGA-GBM MRQy results (XLS)		CC BY 3.0
TCGA-CESC MRQy results (XLS)		CC BY 3.0
CPTAC-GBM MRQy results (XLS)		CC BY 3.0

Click the Versions tab for more info about data releases.

Additional Resources for this Dataset

Source code is available on GitHub at: http://github.com/ccipd/MRQy.

Collections Used in this Third Party Analysis

Below is a list of the Collections used in these analyses:
Some data in this collection contains images that could potentially be used to reconstruct a human face. To safeguard the privacy of participants, users must sign and submit a TCIA Restricted License Agreement to help@cancerimagingarchive.net before accessing the data.

Source Data Type	Download	License
Corresponding Original MR Images from TCGA-GBM (1.37GB) and CPTAC-GBM (DICOM, 0.4 GB)	(Download requires the NBIA Data Retriever and permission)	TCIA Restricted
Corresponding Original MR Images from TCGA-CESC (DICOM, 2.72 GB)	(Download requires the NBIA Data Retriever)	CC BY 3.0

Detailed Description

The spreadsheets provided are derived analyses from subsets of images from the The Cancer Genome Atlas Glioblastoma Multiforme Collection (TCGA-GBM), The Clinical Proteomic Tumor Analysis Consortium Glioblastoma Multiforme Collection (CPTAC-GBM), and The Cancer Genome Atlas Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma Collection (TCGA-CESC) collections. To download the corresponding images for your own analysis you can use the "Source Data Type" table.

Citations & Data Usage Policy

Users must abide by the TCIA Data Usage Policy and Restrictions. Attribution should include references to the following citations:

Data Citation

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

TCIA Citation

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

Other Publications Using This Data

TCIA maintains a list of publications which leverage TCIA data. If you have a manuscript you'd like to add please contact the TCIA Helpdesk.

Version 1 (Current): Updated 2020/07/16

Data Type	Download all or Query/Filter
TCGA-GBM MRQy results (XLS)
TCGA-CESC MRQy results (XLS)
CPTAC-GBM MRQy results (XLS)

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