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title | Data Access |
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| Data Access Tcia license 4 international |
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Note to curators! This macro is for collections that are restricted due to facial reconstruction possibility.
Data Type | Download all or Query/Filter | License |
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Images and Segmentations (NIfTI, 1.4 TB)
| Complete dataset all tasks Tcia button generator |
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complete data on faspex |
(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) | |
| | | BraTS 2021 Segmentation Training set (NIfTI, XX GB )
batch1 (processed from ACRIN-FMISO-Brain) Tcia button generator |
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batch1 |
batch2 (processed from CPTAC GBM) Tcia button generator |
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batch2 |
batch3 (processed from IvyGAP) batch4 (processed from TCGA-GBM) batch5 (processed from TCGA-LGG)batch6 (processed from UPENN-GBM)batch7 (processed from UCSF-PDGM) (Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) | | BraTS 2021 Segmentation Validation set (NIfTI, XX GB) | batch1 (processed from CPTAC GBM) - batch2 (processed from IvyGAP)
batch3 (processed from TCGA-GBM) - batch4 (processed from TCGA-LGG)
- batch5 (processed from UPENN-GBM)
- batch6 (processed from UCSF-PDGM)
(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) | | , XX GB )
| | BraTS 2021 Segmentation Validation Brand new data files not elsewhere on TCIA | (Download and apply the (Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) | TCIA Restricted (special permission beyond defacing DUA required to be fleshed out later) | BraTS 2021 Segmentation Training Brand new data files not elsewhere on TCIA | | BraTS 2021 Validation set (NIfTI, XX GB) |
(Download and apply the the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) | |
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| | | BraTS Task2 Radiogenomics Classifier task Training images (DICOM, GB) | - link to faspex for nifti
- link to GDC/PDC if the detail are there ( e.g. TCGA)
- dicom-->nifti→dicom also on Faspex
| ( is this open license stuff?) | BraTS Task2 Radiogenomics Classifier task molecular marker table (JSON/XLS/CSV spreadsheet, MB) | - download JSON/XLS/CSV spreadsheet or
- if external link that would go below not in this table
| ( is this open license stuff?) | BraTS 2021 Classifier Training Task Brand new data files not elsewhere on TCIA | (Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) | | Complete training ( highest faspex folder) ( folder of BRats2021-CPTAC-GBM) involved in Seg task training ( folder of Brats2021-TCGA-GBM) involved in seg task training | complete validation involved in classifier from xx collection forms a batch here) TCIA | (Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) | |
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| Clinical data (CSV)
| | | Feature matrices (format, ##GB) | | | ID Crosswalk between BraTS ID and TCIA ID (xlsx, 79 kB) |
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url | https://wiki.cancerimagingarchive.net/download/attachments/133073473/BraTS2021_MappingToTCIA.xlsx?api=v2 |
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| BraTS2021_MappingToTCIA |
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Click the Versions tab for more info about data releases. Additional Resources for this Dataset Nci_crdc additional resources |
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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:Source Data Type | Download | License |
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DICOM Used in BraTS 2021 Segmentation Training set from CPTAC-GBM , TCGA-GBM , TCGA-LGG , ACRIN-FMISO-Brain (ACRIN 6684) , IvyGAP ,UPENN-GBM | | 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 , IvyGAP , UPENN-GBM | | 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 , IvyGAP , UPENN-GBM | | 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 , IvyGAP , UPENN-GBM | | 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 IvyGAP |
| new trapd-lnk files of only already-used UCSF-PDGM nonDICOM. New package? | Data retriever or Faspex? | tcia-cc-by-4files (Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) |
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Third Party Analyses of this DatasetTCIA 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>
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title | Detailed Description |
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| Detailed DescriptionImage Statistics | Radiology Image Statistics | Pathology Image Statistics |
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Modalities | MR, Segmentations |
| Number of Patients | 2,040 |
| Number of Studies |
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| Number of Series | 7,131 |
| Number of Images |
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- 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 : BraTS2021_MappingToTCIA.xlsx
- Spreadsheet list of cases and series used in prior year BraTS Challenges which may refer also to these:
- 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 |
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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.
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title | Citations & Data Usage Policy |
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| Citations & Data Usage Policy Tcia limited license policy |
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Info |
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| DOI goes here. Create using Datacite with information from Collection Approval form 44 authors, most with ORCiD.
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Info |
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title | Publication Citation |
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| U.Baid, et al., The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification arXiv:2107.02314, 2021. |
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| "The results <published or shown> here are in whole or part based upon data generated by the TCGA Research Network: http://cancergenome.nih.gov/."
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| 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. In Journal of Digital Imaging (Vol. 26, Issue 6, pp. 1045–1057). Springer Science and Business Media LLC.https://doi.org/10.1007/s10278-013-9622-7 |
Other Publications Using This DataTCIA 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: - Baid, U., et al., The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification, arXiv:2107.02314, 2021.
- 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
- 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:- 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
- 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
- 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
- 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
- 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
- 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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| Version X (Current): Updated yyyy/mm/ddcopy Access tab table here << One or two sentences about what you changed since last version. No note required for version 1. >> |
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