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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

results

measures were generated

for

for 

  1. T1-weighted post-contrast axial MRI sequences from 133 The Cancer Genome Atlas Glioblastoma Multiforme Collection (TCGA-GBM
subjects for whom a
  1. ) subjects 
  2. T1-weighted
POST sequence in the axial plane was available, resulting in a cohort of n=133 T1-POST MRI scans accrued from 7 different sites. All 133 T1-POST studies
  1. post-contrast axial MRI sequences from 46 The Clinical Proteomic Tumor Analysis Consortium Glioblastoma Multiforme Collection (CPTAC-GBM) subjects  
  2. 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


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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
Images (DICOM)

Image Removed

(Requires  NBIA Data Retriever)

MRQy results (XLS)
MRQy results (49 kb, XLSX)


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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 (49 kb, XLSX)


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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 (21 kb, XLSX)


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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)

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Localtab
titleDetailed Description

Detailed Description

The spreadsheet provided is a subset of data from the TCGA-GBM collection. To download the data, please visit the collection page and follow the instructions under the Data Access tab. If you have any questions or issues, please contact help@cancerimagingarchive.net  with any questions regarding usage. 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 please see the "Source Data Type" table.




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.




Image Removed
Localtab
titleVersions

Version 1 (Current): Updated 2020/

04

07/

06

16

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

Image Removed

MRQy results (XLS)
MRQy results (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 (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 (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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