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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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Summary

Redirect
delay5
locationhttps://www.cancerimagingarchive.net/collection/upenn-gbm/

Excerpt

Image Added

This collection comprise comprises multi-parametric magnetic resonance imaging (mpMRI) scans for de novo Glioblastoma (GBM) patients from the Hospital of the University of Pennsylvania Health System, coupled with patient demographics, clinical outcome (e.g., overall survival, progression free survival, molecular alterations of 50 clinically-relevant genes based on a novel next generation sequencing panel, 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. Pre-operative scans defined via radiological assessment for prior surgical instrumentation. 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 an 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, as well as spatial information and diffusion properties extracted from glioma growth models. The generated computer-aided and manually-revised . 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.

Acknowledgements

We would like to acknowledge the individuals and institutions that have provided data for this collection:

...

Additional data accompanying the UPENN-GBM data collection include H&E-stained digitized tissue sections from resected tumor specimens of matched de novo and recurrent cases for a few of the patients in this collection.

Acknowledgements

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.

Localtab Group


Localtab
activetrue
titleData Access

Data Access

Data TypeDownload all or Query/FilterLicense

Images

, Segmentations, and Radiation Therapy Structures/Doses/Plans

(DICOM,

XX

 139.

X

4 GB)

<< latter two items only if DICOM SEG/RTSTRUCT/RTDOSE/PLAN exist >>

Image RemovedImage Removed


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/70225642/UPENN-GBM_DownloadManifest20221129.tcia?api=v2



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



(Download requires the NBIA Data Retriever)

Tissue Slide

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Images (

SVS, XX.X GB)

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Clinical data (CSV)

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Genomics (web)

NIfTI, 69 GB) 


Tcia button generator
urlhttps://faspex.cancerimagingarchive.net/aspera/faspex?context=eyJyZXNvdXJjZSI6InBhY2thZ2VzIiwidHlwZSI6ImV4dGVybmFsX2Rvd25sb2FkX3BhY2thZ2UiLCJpZCI6IjYwNCIsInBhc3Njb2RlIjoiYzJiMjI2Mzg5ZjljYWE0NWNkYjc4MzM4NWE4Yzc2MjBjNGU1NDY1MiIsInBhY2thZ2VfaWQiOiI2MDQiLCJlbWFpbCI6ImhlbHBAY2FuY2VyaW1hZ2luZ2FyY2hpdmUubmV0In0=



(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) 

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Histopathology Images (NDPI, 149 GB)


Tcia button generator
urlhttps://faspex.cancerimagingarchive.net/aspera/faspex?context=eyJyZXNvdXJjZSI6InBhY2thZ2VzIiwidHlwZSI6ImV4dGVybmFsX2Rvd25sb2FkX3BhY2thZ2UiLCJpZCI6IjUwOSIsInBhc3Njb2RlIjoiNTkyMmNjY2U5Nzc5N2YxZTQ2NGIwMWNiMjY0NzQzMjg3YjY4MDA2NiIsInBhY2thZ2VfaWQiOiI1MDkiLCJlbWFpbCI6ImhlbHBAY2FuY2VyaW1hZ2luZ2FyY2hpdmUubmV0In0=



Tcia button generator
labelSearch
urlhttps://pathdb.cancerimagingarchive.net/imagesearch?f[0]=collection:upenn_gbm



(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) 

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Clinical Data (CSV, 51 kB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/70225642/UPENN-GBM_clinical_info_v1.2.csv?api=v2



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Histopathology to Radiology Filename Mapping (CSV, 2 kB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/70225642/radiology_mapping.csv?version=2&modificationDate=1666634570946&api=v2



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Image acquisition parameters (CSV, 195 kB)


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



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Data availability per subject (CSV, 126 kB)


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



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CaPTk radiomic features list (CSV, 6 kB)


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urlhttps://wiki.cancerimagingarchive.net/download/attachments/70225642/UPENN-GBM_CaPTk_radiomic_features_list.csv?api=v2



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CaPTk radiomic feature parameter file (CSV, 4 kB)


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



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Radiomic Data (ZIP,15.37 MB)


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



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Image Removed

Click the Versions tab for more info about data releases.

Please contact help@cancerimagingarchive.net  with any questions regarding usage.

Nci_crdc additional resources


Localtab
titleDetailed Description

Detailed Description

Image Statistics



Modalities

MR

Pathology

Number of Patients

630

34

Number of Studies

3,301

N/A

Number of Series

3,680

N/A

Number of Images

828,234

71

Images Size (GB)
<< Add any additional information as needed below. Likely would be something from site. >>
139.4149


Note from the submitting group:  The NIfTI images are all registered to a common atlas (SRI) using a uniform preprocessing and the segmentation are aligned with them. Therefore the NIfTI images will not align with the DICOM images, by design. If you load the NIfTI images (like T1/T2) and their related segmentation, these will line up.


Localtab
titleCitations & Data Usage Policy

Citations & Data Usage Policy

Add any special restrictions in here.

These collections are freely available to browse, download, and use for commercial, scientific and educational purposes as outlined in the Creative Commons Attribution 4.0 International License. Questions may be directed to help@cancerimagingarchive.net. Please be sure to acknowledge both this data set and TCIA in publications by including the following citations in your work:

Info
titleData Citation

DOI goes here. Create using Datacite with information from Collection Approval form

Info
titlePublication Citation

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

Tcia limited license policy

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., Binder, Z. A., Verma, R., … Davatzikos, C. (2021). Multi-parametric magnetic resonance imaging (mpMRI) scans for de novo Glioblastoma (GBM) patients from the University of Pennsylvania Health System (UPENN-GBM) (Version 2) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.709X-DN49


Info
titlePublication 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., Binder, Z. A., Verma, R., Lustig, R., Desai, A. S., Bagley, S. J., Mourelatos, Z., Morrissette, J., Watt, C. D., Brem, S., Wolf, R. L., Melhem, E. R., Nasrallah, M. P., Mohan, S., O’Rourke, D. M., Davatzikos, C. (2022). The University of Pennsylvania glioblastoma (UPenn-GBM) cohort: advanced MRI, clinical, genomics, & radiomics. In Scientific Data (Vol. 9, Issue 1). https://doi.org/10.1038/s41597-022-01560-7

Info
titleAcknowledgement

Only if they ask for special acknowledgments like funding sources, grant numbers, etc in their proposal.


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 data. If you have a manuscript you'd like to add please contact the TCIA Helpdesk.


<< One or two sentences about what you changed since last version.  No note required for version 1. >> 
Localtab
titleVersions

Version

X

2 (Current):

Updated yyyy/mm/dd

2022/10/24

Note: 2023/12/5: updated clinical data file (v1.2) to include more information about censor/survival.

Data TypeDownload all or Query/FilterLicense

Images (DICOM,

xx

 139.

x GB)

Image RemovedImage Removed

(Requires NBIA Data Retriever.)

Clinical Data (CSV)Link
Other (format)

Image Removed

4 GB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/70225642/UPENN-GBM_DownloadManifest20221129.tcia?api=v2



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



(Download requires the NBIA Data Retriever)

Tcia cc by 4

Images (NIfTI, 69 GB) 


Tcia button generator
urlhttps://faspex.cancerimagingarchive.net/aspera/faspex?context=eyJyZXNvdXJjZSI6InBhY2thZ2VzIiwidHlwZSI6ImV4dGVybmFsX2Rvd25sb2FkX3BhY2thZ2UiLCJpZCI6IjYwNCIsInBhc3Njb2RlIjoiYzJiMjI2Mzg5ZjljYWE0NWNkYjc4MzM4NWE4Yzc2MjBjNGU1NDY1MiIsInBhY2thZ2VfaWQiOiI2MDQiLCJlbWFpbCI6ImhlbHBAY2FuY2VyaW1hZ2luZ2FyY2hpdmUubmV0In0=



(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) 

Tcia cc by 4

Histopathology Images (NDPI, 149 GB)


Tcia button generator
urlhttps://faspex.cancerimagingarchive.net/aspera/faspex?context=eyJyZXNvdXJjZSI6InBhY2thZ2VzIiwidHlwZSI6ImV4dGVybmFsX2Rvd25sb2FkX3BhY2thZ2UiLCJpZCI6IjUwOSIsInBhc3Njb2RlIjoiNTkyMmNjY2U5Nzc5N2YxZTQ2NGIwMWNiMjY0NzQzMjg3YjY4MDA2NiIsInBhY2thZ2VfaWQiOiI1MDkiLCJlbWFpbCI6ImhlbHBAY2FuY2VyaW1hZ2luZ2FyY2hpdmUubmV0In0=



Tcia button generator
labelSearch
urlhttps://pathdb.cancerimagingarchive.net/imagesearch?f[0]=collection:upenn_gbm


(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) 

Tcia cc by 4

Clinical Data (CSV, 51 kB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/70225642/UPENN-GBM_clinical_info_v1.2.csv?api=v2



Tcia cc by 4

Histopathology to Radiology Filename Mapping (CSV, 2kB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/70225642/radiology_mapping.csv?version=1&modificationDate=1666627440627&api=v2



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Image acquisition parameters (CSV, 195 kB)


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



Tcia cc by 4

Data availability per subject (CSV, 126 kB)


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



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CaPTk radiomic features list (CSV, 6 kB)


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



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CaPTk radiomic feature parameter file (CSV, 4 kB)


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



Tcia cc by 4

Radiomic Data (ZIP,15.37 MB)


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



Tcia cc by 4

changes: Histopathology NDPI slides added to collection. CSV file for mapping Radiology subject IDs to Histopathology patient and image IDs where available (note: not all Radiology data has associated pathology data and vice versa).

Version 1: 2022/06/21

Data TypeDownload all or Query/FilterLicense

Images (DICOM, 139.4 GB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/70225642/UPENN-GBM-manifest_20210923.tcia?api=v2



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



(Download requires the NBIA Data Retriever)

Tcia cc by 4

Images (NIfTI, 69 GB) 


Tcia button generator
urlhttps://faspex.cancerimagingarchive.net/aspera/faspex?context=eyJyZXNvdXJjZSI6InBhY2thZ2VzIiwidHlwZSI6ImV4dGVybmFsX2Rvd25sb2FkX3BhY2thZ2UiLCJpZCI6IjYwNCIsInBhc3Njb2RlIjoiYzJiMjI2Mzg5ZjljYWE0NWNkYjc4MzM4NWE4Yzc2MjBjNGU1NDY1MiIsInBhY2thZ2VfaWQiOiI2MDQiLCJlbWFpbCI6ImhlbHBAY2FuY2VyaW1hZ2luZ2FyY2hpdmUubmV0In0=



(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) 

Tcia cc by 4

Clinical Data (CSV, 51 kB)


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



Tcia cc by 4

Image acquisition parameters (CSV, 195 kB)


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



Tcia cc by 4

Data availability per subject (CSV, 126 kB)


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



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CaPTk radiomic features list (CSV, 6 kB)


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urlhttps://wiki.cancerimagingarchive.net/download/attachments/70225642/UPENN-GBM_CaPTk_radiomic_features_list.csv?api=v2



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CaPTk radiomic feature parameter file (CSV, 4 kB)


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



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Radiomic Data (ZIP,15.37 MB)


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



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CaPTk radiomic feature parameter (CSV, 5KB)


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urlhttps://wiki.cancerimagingarchive.net/download/attachments/70225642/captk_parameter_file_ispy1.csv?api=v2



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