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title | Data Access |
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| Data AccessNote to curators! This macro is for collections that are restricted due to facial reconstruction possibility. "DICOM and NIFTI for all imaging data, and CSV for clinical and genomic data" Clinical, Image Analyses, Image Registrations, Genomics, Software/Source Code, Radiomic Features
Complete dataset Data Type | Download all or Query/Filter | License |
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Images, Segmentations (NIfTI, 1.4 TB) Challenge data both tasks (142 GB, 1480 patients, NIfTI, DICOM) | |
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url | https://faspex.cancerimagingarchive.net/aspera/faspex?context=eyJyZXNvdXJjZSI6InBhY2thZ2VzIiwidHlwZSI6ImV4dGVybmFsX2Rvd25sb2FkX3BhY2thZ2UiLCJpZCI6IjYzNiIsInBhc3Njb2RlIjoiNDM5YTVhZjM3NGRhYjk3OGExYjExMzA4MTcyZDhlMDdkY2Q5OWMzMSIsInBhY2thZ2VfaWQiOiI2MzYiLCJlbWFpbCI6ImhlbHBAY2FuY2VyaW1hZ2luZ2FyY2hpdmUubmV0In0= |
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| complete Challenge data on faspex |
(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) | |
BraTS 2021 Training set in batches of XXX PatientID Images, Segmentations (NIfTI, 1.4 TB) | batch1 (ID PP to QQ) | ID Crosswalk between BraTS ID and TCIA ID (xlsx, 79 kB) | |
batch1 | batch2 (ID XX to YY) Tcia button generator |
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(and so on) (Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) | BraTS 2021 Validation set in batches of XXX PatientID Images, Segmentations (NIfTI, 1.4 TB)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. Collections Used in this Third Party AnalysisBelow is a list of the Collections used in these analyses. Be sure to include "RSNA-ASNR-MICCAI-BraTS-2021 DOI: 10.7937/jc8x-9874" in the COLLECTION section of your form to assure the request is processed appropriately. Source Data Type | Download | License |
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Original corresponding DICOM used in BraTS 2021 Segmentation Training set from CPTAC-GBM , TCGA-GBM , TCGA-LGG , ACRIN-FMISO-Brain (ACRIN 6684) , IvyGAP ,UPENN-GBM | |
batch1 | Tcia button generator |
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(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) | BraTS Task2 Radiogenomics Classifier task images (DICOM?, GB) | - link to faspex for nifti
- link to GDC/PDC if the detail are there
| ( is this open license stuff?) | BraTS Task2 Radiogenomics Classifier task molecular marker table (JSON/XLS/CSV spreadsheet, MB) | - download JSON/XLS/CSV spreadsheet or
- external link to RSNA/Kaggle's accompanying molecular marker table , depending on how they want to do that
| ( is this open license stuff?) | Images from TCGA-LGG that have been transformed for use in this challenge - 108 Subjects (DICOM, 8.url | https://wiki.cancerimagingarchive.net/download/attachments/133073473/BraTS2021_TCIAderived_Seg-Task-Training.tcia?api=v2 |
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| seg train |
Download requires the NBIA Data Retriever | | Original corresponding DICOM used in BraTS 2021 MGMT Classifier Training set from CPTAC-GBM , TCGA-GBM , IvyGAP , UPENN-GBM | 5 GB) |
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url | https://wiki.cancerimagingarchive.net/download/attachments/ |
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| 24282668/doiJNLP-JAMS4RFqClick the Download button to save a ".tcia" manifest file to your computer, which you must open with the 133073473/BraTS2021_TCIAderived_Class-Task-Training.tcia?api=v2 |
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| Note: Limited Access. . Images from TCGA-GBM that have been transformed for use in this challenge- 135 subjects (DICOM, 6 GB)Original corresponding DICOM used in BraTS 2021 Segmentation Validation set from CPTAC-GBM , TCGA-GBM , TCGA-LGG , IvyGAP , UPENN-GBM |
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url | https://wiki.cancerimagingarchive.net/download/attachments/ |
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| 24282666/doiJNLP-QoOaKUdnClick the Download button to save a ".tcia" manifest file to your computer, which you must open with the 133073473/BraTS2021_TCIAderived_Seg-Task-Validation.tcia?api=v2 |
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| Note: Limited Access.Images from Ivy GAP that have been transformed for use in this challenge- XXX subjects (DICOM, XX GB)Original corresponding DICOM used in BraTS 2021 MGMT Classifier Validation set from CPTAC-GBM , TCGA-GBM , IvyGAP , UPENN-GBM | | Ivy GAPClick the Download button to save a ".tcia" manifest file to your computer, which you must open with the Note: Limited Access.https://wiki.cancerimagingarchive.net/download/attachments/133073473/BraTS2021_TCIAderived_Class-Task-Validation.tcia?api=v2 |
| class valid |
Download requires the | CPTAC-GBM DICOMOriginal corresponding imaging from UCSF-PDGM v1 | | restricted-licenseUCSF-PDGM DICOM (note Evan didn't give this to us – only nifti so far) | UPENN-GBM DICOM ( others) | Transformation matrices DICOM to NII (zip, XXMB) | Tcia button generator |
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| Clinical data (CSV) Tcia button generator |
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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. | | Click the Versions tab for more info about data releases. Additional Resources for this DatasetNote to curators! Use this any time you are linking to NCI's IDC/GDC/PDC resources. The links below are examples and will need to be tailored to point to the specific dataset (see parameters in URLS). button-generator |
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url | https://faspex.cancerimagingarchive.net/aspera/faspex?context=eyJyZXNvdXJjZSI6InBhY2thZ2VzIiwidHlwZSI6ImV4dGVybmFsX2Rvd25sb2FkX3BhY2thZ2UiLCJpZCI6IjY3OSIsInBhc3Njb2RlIjoiZmEwODZjMDQyNGNkOGM4OTllZTRjY2VmZTE0ZGUyM2FkMjA3N2M5NSIsInBhY2thZ2VfaWQiOiI2NzkiLCJlbWFpbCI6ImhlbHBAY2FuY2VyaW1hZ2luZ2FyY2hpdmUubmV0In0= |
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(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) | CC BY 4.0 |
Additional Resources for this DatasetThe NCI Cancer Research Data Commons (CRDC) provides access to additional data and a cloud-based data science infrastructure that connects data sets with analytics tools to allow users to share, integrate, analyze, and visualize cancer research data.nci_crdc-additional-resources 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
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 | Modalities | Number of Patients | 1,480 | Number of Studies |
| Number of Series | 7,131 | Number of Images | 407,245 | Images Size (GB) | 140 |
NOTE: The "challenge test set dataset" is sequestered on synapse.org (Project SynID: syn25829067). Please see their site for more detail. NOTE: Segmentation task nifti: Number of Images 7,131 (Seg) , Images Size (GB)12 (Seg) NOTE: Classification task nifti+DICOM: Number of Images 400,114 (Class), Images Size (GB) 128 (Class) Segmentation labels of the different glioma sub-regions considered for evaluation are the "enhancing tumor" (ET), the "tumor core" (TC), and the "whole tumor" (WT). The ET is described by areas that show hyper-intensity in T1Gd when compared to T1, but also when compared to “healthy” white matter in T1Gd. The TC describes the bulk of the tumor, which is what is typically resected. The TC entails the ET, as well as the necrotic (NCR) << Add any additional information that didn't fit or belong in the Summary section. >>parts of the tumor. The appearance of NCR is typically hypo-intense in T1-Gd when compared to T1. The WT describes the complete extent of the disease, as it entails the TC and the peritumoral edematous/invaded tissue (ED), which is typically depicted by hyper-intense signal in FLAIR. The provided segmentation labels have values of 1 for NCR, 2 for ED, 4 for ET, and 0 for everything else. 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: - Manifest of case identifiers between BraTS and TCIA, NOTE: includes new series files with no TCIA equivalent: BraTS2021_MappingToTCIA.xlsx
- Spreadsheet list of cases and series used in prior year BraTS Challenges may also refer to these:
Notes about Image Registration:- Transformation matrices DICOM to NIfTI are not available.
- Segmentation task image volume have been set to x=y=240 voxels by z=155 voxels.
- All Radiogenomics Classifier task files are restored to original DICOM resolution & orientation (thus volume may vary).
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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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| Baid, U., Ghodasara, S., Mohan, S., Bilello, M., Calabrese, E., Colak, E., Farahani, K., Kalpathy-Cramer, J., Kitamura, F. C., Pati, S., Prevedello, L., Rudie, J., Sako, C., Shinohara, R., Bergquist, T., Chai, R., Eddy, J., Elliott, J., Reade, W., Schaffter, T., Yu, T., Zheng, J., Davatzikos, C., Mongan, J., Hess, C., Cha, S., Villanueva-Meyer, J., Freymann, J. B., Kirby, J. S., Wiestler, B., Crivellaro, P., Colen, R. R., Kotrotsou, A., Marcus, D., Milchenko, M., Nazeri, A., Fathallah-Shaykh, H., Wiest, R., Jakab, A., Weber, M-A., Mahajan, A., Menze, B., Flanders, A E., Bakas, S., (2023) RSNA-ASNR-MICCAI-BraTS-2021 Dataset. The Cancer Imaging Archive DOI: 10.7937/jc8x-9874 |
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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/."DOI goes here. Create using Datacite with information from Collection Approval form |
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title | Publication Citation |
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| 1. Baid, U.Baid, et al., "., Ghodasara, S., Mohan, S., Bilello, M., Calabrese, E., Colak, E., Farahani, K., Kalpathy-Cramer, J., Kitamura, F. C., Pati, S., Prevedello, L. M., Rudie, J. D., Sako, C., Shinohara, R. T., Bergquist, T., Chai, R., Eddy, J., Elliott, J., Reade, W., Schaffter, T., Yu, T., Zheng, J., Moawad, A. W., Coelho, L. O., McDonnell, O., Miller, E., Moron, F. E., Oswood, M. C., Shih, R. Y., Siakallis, L., Bronstein, Y., Mason, J. R., Miller, A. F., Choudhary, G., Agarwal, A., Besada, C. H., Derakhshan, J. J., Diogo, M. C., Do-Dai, D D., Farage, L., Go, J. L., Hadi, M., Hill, V. B., Iv, M., Joyner, D., Lincoln, C., Lotan, E., Miyakoshi, A., Sanchez-Montano, M., Nath, J., Nguyen, X. V., Nicolas-Jilwan, M., Ortiz Jimenez, J., Ozturk, K., Petrovic, B. D., Shah, C., Shah, L. M., Sharma, M., Simsek, O., Singh, A. K., Soman, S., Statsevych, V., Weinberg, B. D., Young, R. J., Ikuta, I., Agarwal, A. K.,Cambron, S. C., Silbergleit, R., Dusoi, A., Postma, A. A., Letourneau-Guillon, L., Guzman Perez-Carrillo, G. J., Saha, A., Soni, N., Zaharchuk, G., Zohrabian, V. M., Chen, Y., Cekic, M. M., Rahman, A., Small, J. E., Sethi, V., Davatzikos, C., Mongan, J., Hess, C., Cha, S., Villanueva-Meyer, J., Freymann, J. B., Kirby, J. S., Wiestler, B., Crivellaro, P., Colen, R. R., Kotrotsou, A., Marcus, D., Milchenko, M., Nazeri, A., Fathallah-Shaykh, H., Wiest, R., Jakab, A., Weber, M-A. Mahajan ,A., Menze, B., Flanders, A. E., Bakas, S. (2021). The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification", arXiv:2107.02314, 2021. (Version 2). arXiv. DOI: 10.48550/arXiv.2107.02314
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You are free to use and/or refer to the BraTS datasets in your own research, provided that you always cite the flagship manuscript above resulting from the challenge as well as the following two manuscripts:
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title | Publication Citation |
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| 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). DOI: 10.1109/tmi.2014.2377694 |
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title | Acknowledgement | Publication Citation |
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| 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.2017.117Required acknowledgements only (ex:The CPTAC program requests that publications using data from this program...). If they just want to thank someone, that goes in the Acknowledgement section underneath the Summary. |
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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 |
Additional Publication Resources:The Collection authors suggest the below will give context to this dataset: You are free to use and/or refer to the BraTS datasets in your own research. 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) (Version 1) [Data set]. The Cancer Imaging Archive. https://doi.org/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
Other Publications Using This DataTCIA 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. |
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| Version X 1 (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. >> 2023/08/25Data Type | Download all or Query/Filter | License |
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Challenge data (both tasks, 142 GB, *.nii.gz or *.dcm) |
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url | https://faspex.cancerimagingarchive.net/aspera/faspex?context=eyJyZXNvdXJjZSI6InBhY2thZ2VzIiwidHlwZSI6ImV4dGVybmFsX2Rvd25sb2FkX3BhY2thZ2UiLCJpZCI6IjYzNiIsInBhc3Njb2RlIjoiNDM5YTVhZjM3NGRhYjk3OGExYjExMzA4MTcyZDhlMDdkY2Q5OWMzMSIsInBhY2thZ2VfaWQiOiI2MzYiLCJlbWFpbCI6ImhlbHBAY2FuY2VyaW1hZ2luZ2FyY2hpdmUubmV0In0= |
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| complete Challenge data on faspex |
(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) | | 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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