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  • Multi-parametric magnetic resonance imaging (mpMRI) scans for de novo Glioblastoma (GBM) patients from the University of Pennsylvania Health System (UPENN-GBM)

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Excerpt

This collection comprises multi-parametric magnetic resonance imaging (mpMRI) scans for de novo Glioblastoma (GBM) patients from the Hospital of the University of Pennsylvania, coupled with patient demographics, clinical outcome (e.g., overall survival, genomic information, tumor progression), as well as computer-aided and manually-corrected segmentation labels of multiple histologically distinct tumor sub-regions, computer-aided and manually-corrected segmentations of the whole brain, a rich panel of radiomic features along with their corresponding co-registered mpMRI volumes in NIfTI format. Scans were initially skull-stripped and co-registered, before their tumor segmentation labels were produced by an automated computational method. These segmentation labels were revised and any label misclassifications were manually corrected/approved by expert board-certified neuroradiologists. The final labels were used to extract a rich panel of imaging features, including intensity, volumetric, morphologic, histogram-based and textural parameters. The segmentation labels enable quantitative computational and clinical studies without the need to repeat manual annotations whilst allowing for comparison across studies. They can also serve as a set of manually-annotated gold standard labels for performance evaluation in computational challenges. The provided panel of radiomic features may facilitate research integrative of the molecular characterization offered, and hence allow associations with molecular markers (radiogenomic biomarker research), clinical outcomes, treatment responses and other endpoints, by researchers without sufficient computational background to extract such features.

Acknowledgement

Reported research was partly supported by the National Cancer Institute (NCI), the National Institute of Neurological Disorders and Stroke (NINDS), and the National Center for Advancing Translational Sciences (NCATS) of the National Institutes of Health (NIH) under award numbers NINDS:R01NS042645, NCI:U24CA189523, NCI:U01CA242871, NCATS:UL1TR001878, and by the Institute for Translational Medicine and Therapeutics (ITMAT) of the University of Pennsylvania. The content of this publication is solely the responsibility of the authors and does not represent the official views of the NIH, or the ITMAT of the UPenn.

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Localtab
activetrue
titleData Access

Data Access

Click the Download button to save a ".tcia" manifest file to your computer, which you must open with the NBIA Data Retriever. Click the Search button to open our Data Portal, where you can browse the data collection and/or download a subset of its contents.

Data TypeDownload all or Query/Filter

Images (DICOM, 139.4 GB)

Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/70225642/UPENN-GBM-manifest_20210810.tcia?api=v2

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labelSearch
urlhttps://nbia.cancerimagingarchive.net/nbia-search/?MinNumberOfStudiesCriteria=1&CollectionCriteria=UPENN-GBM

(Download requires the NBIA Data Retriever)

Clinical Data (CSV, 51 kB)

Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/70225642/UPENN-GBM_clinical_info_v1.0.csv?api=v2

Radiomic Data (ZIP,15.37 MB)

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urlhttps://wiki.cancerimagingarchive.net/download/attachments/70225642/radiomic_features_CaPTk.zip?api=v2

Images (NIfTI, 69 GB) 

Tcia button generator
exttrue
urlhttps://faspex.cancerimagingarchive.net/aspera/faspex/external_deliveries/181?passcode=639c82e9a59d8f3b60dd1f039d68e7d09bf1b404

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Localtab
titleDetailed Description

Detailed Description

Image Statistics


Modalities

MR

Number of Patients

630

Number of Studies

3,301

Number of Series

3,680

Number of Images

828,234

Images Size (GB)139.4



Localtab
titleCitations & Data Usage Policy

Citations & Data Usage Policy

Public collection license

Info
titleData Citation

Bakas, S., Sako, C., Akbari, H., Bilello, M., Sotiras, A., Shukla, G., Rudie, J. D., Flores Santamaria, N., Fathi Kazerooni, A., Pati, S., Rathore, S., Mamourian, E., Ha, S. M., Parker, W., Doshi, J., Baid, U., Bergman, M., Verma, R., Lustig, R., … Davatzikos, C. (2021). Multi-parametric magnetic resonance imaging (mpMRI) scans for de novo Glioblastoma (GBM) patients from the Hospital of the University of Pennsylvania [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.709X-DN49


Info
titlePublication Citation

We ask on the proposal form if they have ONE traditional publication they'd like users to cite.


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, 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.


Localtab
titleVersions

Version 1 (Current): 2021/00/00

Data TypeDownload all or Query/Filter
Images (DICOM, 139.4 GB)

Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/70225642/UPENN-GBM-manifest_20210810.tcia?api=v2

Tcia button generator
labelSearch
urlhttps://nbia.cancerimagingarchive.net/nbia-search/?MinNumberOfStudiesCriteria=1&CollectionCriteria=UPENN-GBM

(Requires NBIA Data Retriever.)

Clinical Data (CSV, 51 kB)

Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/70225642/UPENN-GBM_clinical_info_v1.0.csv?api=v2

Radiomic Data (ZIP,15.37 MB)

Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/70225642/radiomic_features_CaPTk.zip?api=v2

Images (NIfTI, 69 GB) 

Tcia button generator
exttrue
urlhttps://faspex.cancerimagingarchive.net/aspera/faspex/external_deliveries/181?passcode=639c82e9a59d8f3b60dd1f039d68e7d09bf1b404



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