Page History

Data Access

Note to curators! This macro is for collections that are restricted due to facial reconstruction possibility.

Click the Versions tab for more info about data releases.

Additional Resources for this Dataset

• Imaging Data Commons (IDC) (Imaging Data)
• Proteomic Data Commons (PDC) (Proteomic & Clinical Data)
  • TCGA-GBM
• Genomic Data Commons (GDC) (Genomic & Clinical Data)
  • TCGA-GBM

Note to curators! Below are examples for what to do with other external resources/links that don't fit into the above categories.

The following external resources have been made available by the data submitters.  These are not hosted or supported by TCIA, but may be useful to researchers utilizing this collection.

• Software / Code on Github
• Genomics data in DbGAP
• Genomics data in Gene Expression Omnibus
• RSNA or kaggle link to molecular marker table if they only provide us a link

TCIA Collections Used (in part) in these analyses:

Third Party Analyses of this Dataset

TCIA encourages the community to publish your analyses of our datasets. Below is a list of such third party analyses published using this Collection:

• <these get filled in as groups cite the dataset in their papers related to analysis of the 2021 task 1 & task2 using this Collection's DOI>

Detailed Description

•  the "challenge test set dataset" is sequestered on synapse as a tarball of nii & seg & age & diagnosis. Not available. Please see <website> for more detail.

The data used in BraTS Challenges often have some overlap with other TCIA Collections, cases, and series. Some filters for handling these, so that you can work with statistically not-duplicated images, include these below:

• Manifests of case identifiers between BraTS and TCIA
• Spreadsheet list of cases and series used in prior year BraTS Challenges  which may refer also to these:
  • Multimodal Brain Tumor Segmentation Challenge 2018 (BraTS)
  • Multimodal Brain Tumor Segmentation Challenge 2019
  • Segmentation Labels and Radiomic Features for the Pre-operative Scans of the TCGA-GBM collection (BraTS-TCGA-GBM)
  • Segmentation Labels and Radiomic Features for the Pre-operative Scans of the TCGA-LGG collection (BraTS-TCGA-LGG)
• Spreadsheet list of new (DICOM and NIFTI) series files with no TCIA DICOM equivalent: 

•  Here are some data splits that you might find useful. Manifest of (DICOM and NIFTI) files sourced from other TCIA Collections, so you can avoid superset accidental duplication in case you want everything TCIA has, after you've gotten all of BRaTS data

  Source Data Type	Download	License
  DICOM Used in BraTS 2021 Segmentation Training set from  CPTAC-GBM , TCGA-GBM , TCGA-LGG , ACRIN-FMISO-Brain (ACRIN 6684) , IvyGAP ,	Note: Limited Access. Download requires the NBIA Data Retriever	Tcia restricted license To get data used in BraTS-2021 please request the following Collections in your Agreement: CPTAC-GBM , TCGA-GBM , TCGA-LGG , ACRIN-FMISO-Brain (ACRIN 6684) , IvyGAP
  DICOM Used in BraTS 2021 Classifier Training set from  CPTAC-GBM , TCGA-GBM , TCGA-LGG , ACRIN-FMISO-Brain (ACRIN 6684) , IvyGAP ,	Note: Limited Access. Download requires the NBIA Data Retriever	Tcia restricted license To get data used in BraTS-2021 please request the following Collections in your Agreement: CPTAC-GBM , TCGA-GBM , TCGA-LGG , ACRIN-FMISO-Brain (ACRIN 6684) , IvyGAP
  DICOM Used in BraTS 2021 Segmentation Validation set from  CPTAC-GBM , TCGA-GBM , TCGA-LGG , ACRIN-FMISO-Brain (ACRIN 6684) , IvyGAP ,	Note: Limited Access. Download requires the NBIA Data Retriever	Tcia restricted license To get data used in BraTS-2021 please request the following Collections in your Agreement: CPTAC-GBM , TCGA-GBM , TCGA-LGG , ACRIN-FMISO-Brain (ACRIN 6684) , IvyGAP
  DICOM Used in BraTS 2021 Classifier Validation set from  CPTAC-GBM , TCGA-GBM , TCGA-LGG , ACRIN-FMISO-Brain (ACRIN 6684) , IvyGAP ,	Note: Limited Access. Download requires the NBIA Data Retriever	Tcia restricted license To get data used in BraTS-2021 please request the following Collections in your Agreement: CPTAC-GBM , TCGA-GBM , TCGA-LGG , ACRIN-FMISO-Brain (ACRIN 6684) , IvyGAP
  UCSF-PDGM  DICOM	Data retriever or Faspex?	Tcia cc by 4
  UPENN-GBM DICOM	Data retriever or Faspex?	Tcia cc by 4
  Images from TCGA-LGG that have been transformed for use in this challenge  - 108 Subjects (DICOM, 8.5 GB)	Tcia button generator url https://wiki.cancerimagingarchive.net/download/attachments/24282668/doiJNLP-JAMS4RFq.tcia?api=v2 TCGA-LGG batch1 source series Note: Limited Access. Click the Download  button to save a ".tcia" manifest file to your computer, which you must open with the  NBIA Data Retriever .	Tcia restricted license
  Images from TCGA-GBM that have been transformed for use in this challenge- 135 subjects (DICOM, 6 GB)	Tcia button generator url https://wiki.cancerimagingarchive.net/download/attachments/24282666/doiJNLP-QoOaKUdn.tcia?api=v2 TCGA-GBM batch1 source series Note: Limited Access. Click the Download  button to save a ".tcia" manifest file, needs the NBIA Data Retriever	Tcia restricted license
  Images from Ivy GAP that have been transformed for use in this challenge- XXX subjects (DICOM, XX GB)	Tcia button generator Ivy GAP batch1 source series Note: Limited Access. Click the Download  button to save a ".tcia" manifest file, needs the  NBIA Data Retriever	Tcia restricted license

  
  

Note: Transformation matrices DICOM to NIfTI are not available. Seg tasks are x/y/z 240/240/155 and all Radiogenomics Classifier files are restored to original DICOM resolution & orientation.

Citations & Data Usage Policy

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.

Copied from the Kaggle site: 

You are free to use and/or refer to the BraTS datasets in your own research, provided that you always cite the flagship manuscript (published or pre-published) resulting from the challenge as well as the following three manuscripts:

1.  Baid, U., et al., The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification, arXiv:2107.02314, 2021.
2. Menze, B. H., Jakab, A., Bauer, S., Kalpathy-Cramer, J., Farahani, K., Kirby, J., Burren, Y., Porz, N., Slotboom, J., Wiest, R., Lanczi, L., Gerstner, E., Weber, M.-A., Arbel, T., Avants, B. B., Ayache, N., Buendia, P., Collins, D. L., Cordier, N., … Van Leemput, K. (2015). The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS). In IEEE Transactions on Medical Imaging (Vol. 34, Issue 10, pp. 1993–2024). Institute of Electrical and Electronics Engineers (IEEE). https://doi.org/10.1109/tmi.2014.2377694
3. Bakas, S., Akbari, H., Sotiras, A., Bilello, M., Rozycki, M., Kirby, J. S., Freymann, J. B., Farahani, K., & Davatzikos, C. (2017). Advancing The Cancer Genome Atlas glioma MRI collections with expert segmentation labels and radiomic features. In Scientific Data (Vol. 4, Issue 1). https://doi.org/10.1038/sdata.2017.117
   
   In addition, please be specific and also cite the following datasets that were part of this Challenge:
   1. Bakas, S., Akbari, H., Sotiras, A., Bilello, M., Rozycki, M., Kirby, J., Freymann, J., Farahani, K., & Davatzikos, C. (2017). Segmentation Labels for the Pre-operative Scans of the TCGA-GBM collection [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2017.KLXWJJ1Q
   2. Bakas, S., Akbari, H., Sotiras, A., Bilello, M., Rozycki, M., Kirby, J., Freymann, J., Farahani, K., & Davatzikos, C. (2017). Segmentation Labels for the Pre-operative Scans of the TCGA-LGG collection [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2017.GJQ7R0EF
   3. Scarpace, L., Mikkelsen, T., Cha, S., Rao, S., Tekchandani, S., Gutman, D., Saltz, J. H., Erickson, B. J., Pedano, N., Flanders, A. E., Barnholtz-Sloan, J., Ostrom, Q., Barboriak, D., & Pierce, L. J. (2016). The Cancer Genome Atlas Glioblastoma Multiforme Collection (TCGA-GBM) (Version 4) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2016.RNYFUYE9
   4. Pedano, N., Flanders, A. E., Scarpace, L., Mikkelsen, T., Eschbacher, J. M., Hermes, B., Sisneros, V., Barnholtz-Sloan, J., & Ostrom, Q. (2016). The Cancer Genome Atlas Low Grade Glioma Collection (TCGA-LGG) (Version 3) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2016.L4LTD3TK
   5. Calabrese, E., Villanueva-Meyer, J., Rudie, J., Rauschecker, A., Baid, U., Bakas, S., Cha, S., Mongan, J., & Hess, C. (2022). The University of California San Francisco Preoperative Diffuse Glioma MRI (UCSF-PDGM) [Dataset].  The Cancer Imaging Archive.  https://10.7937/tcia.bdgf-8v37 
   6. 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

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