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

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Summary

Excerpt
These

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

  1. T1-weighted post-contrast axial MRI sequences from
133
  1. 133 The Cancer Genome Atlas Glioblastoma Multiforme Collection (TCGA-GBM
subjects 
  1. ) subjects 
  2. T1-weighted post-contrast axial MRI sequences from
46
  1. 46 The Clinical Proteomic Tumor Analysis Consortium Glioblastoma Multiforme Collection (CPTAC-GBM
subjects  
  1. ) subjects  
  2. Both T1- and T2-weighted axial MRI sequences from
54
  1. 54 The Cancer Genome Atlas Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma Collection (TCGA-CESC
subjects
  1. ) 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).


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


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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).


Localtab Group



Localtab
activetrue
titleData Access

Data Access


Data TypeDownload all or Query/FilterLicense
TCGA-GBM MRQy results (
XLS)Image Removed
49 kb, XLSX)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/70223538/TCGA_GBM_MRQy_Results.xlsx?api=v2

TCGA-GBM MRQy Results.xlsx


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TCGA-CESC MRQy results (
XLS)
49 kb, XLSX)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/70223538/TCGA_CESC%28T1_and_T2%29_MRQy_Results.xlsx?api=v2

TCGA-CESC T1 and T2 MRQy Results.xlsx


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CPTAC-GBM MRQy results (
XLS)
21 kb, XLSX)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/70223538/CPTAC_GBM_MRQy_Results.xlsx

CPTAC-GBM MRQy Results.xlsx


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Click the Versions tab for more info about data releases. Note:   Please contact help@cancerimagingarchive.net  with any questions regarding usage.

Additional Resources for this Dataset

Collections Used in this Third Party Analysis


Below is a list of the Collections used in these analyses:

Tcia head license access

Source Data Type

Download

License

Corresponding Original MR Images from TCGA-GBM  (1.37GB) and CPTAC-GBM (DICOM, 0.4 GB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/140313041/CPTACandTCGA_GBM_MRQy.tcia?api=v2

CombinedHeadRadiology subset used in MRQy

(Download requires the NBIA Data Retriever and permission)

Tcia restricted license

Corresponding Original MR Images from  TCGA-CESC (DICOM, 2.72 GB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/140313041/TCGA_CESC_MRQy.tcia?api=v2

TCGA-CESC subset used in MRQy

(Download requires the NBIA Data Retriever)

Tcia cc by 3





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 help@cancerimagingarchive.net. please see the "Source Data Type" table.

Localtab
titleDetailed Description

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 original corresponding images for your own analysis you can use the table below:

Data TypeDownload all or Query/Filter
TCGA-GBM MRQy Images (DICOM)

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TCGA-CESC MRQy Images (DICOM)

Image Removed

CPTAC-GBM MRQy Images (DICOM)

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Localtab
titleCitations & Data Usage Policy

Citations & Data Usage Policy

public

tcia-

collection

limited-license-policy


Info
titleData Citation

Sadri, A. R., Janowczyk, A., Verma, R., Antunes, J., Madabhushi, A., Tiwari, P., & Viswanath, S. E(2020). MRQy quality measures for TCIA MRI datasets [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2020.JHZ2-T694


Info
titleTCIA 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, Volume 26, Number (6, December, 2013, pp 1045-1057. DOI: ), 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 our data. If you have a manuscript you'd like to add please contact the TCIA's Helpdesk.




Localtab
titleVersions

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

Data TypeDownload all or Query/FilterLicense
TCGA-GBM MRQy results (
XLS)Image Removed
49 kb, XLSX)
Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/70223538/TCGA_GBM_MRQy_Results.xlsx?api=v2

TCGA-GBM MRQy Results.xlsx


Tcia cc by 3

TCGA-CESC MRQy results (
XLS)
49 kb, XLSX)
Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/70223538/TCGA_CESC%28T1_and_T2%29_MRQy_Results.xlsx?api=v2

TCGA-CESC T1 and T2 MRQy Results.xlsx


Tcia cc by 3

Image Removed

CPTAC-GBM MRQy results (
XLS)
21 kb, XLSX)
Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/70223538/CPTAC_GBM_MRQy_Results.xlsx

CPTAC-GBM MRQy Results.xlsx


Tcia cc by 3

Image Removed