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title | Data Access |
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| Data AccessData Type | Download all or Query/Filter | License |
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Images and Annotations (NIfTI format , 156 GB) |
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url | https://faspex.cancerimagingarchive.net/aspera/faspex/external_deliveries/355357?passcode=74fa8e9291ff65e220c994599c6db0c7582f475de722861fdd0278611166a64f0b66e46d9e6ae17c |
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| v3 Download | (Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) | | Clinical data (CSV)
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url | https://wiki.cancerimagingarchive.net/download/attachments/119705830/UCSF-PDGM-metadata_v2.csv?api=v2 |
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Click the Versions tab for more info about data releases. |
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title | Detailed Description |
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| Detailed DescriptionImage Statistics |
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Modalities | MR | Number of Patients | 501495* | Number of Studies | 501 | Number of Files | 11,523 | Images Size (GB) | 156.5 GB |
All image data have been "skull stripped", deidentified, pre-processed per the methods section of our abstract, and converted to NIfTI format. We cannot provide original DICOM data, however, these pre-processed files have been prepared to facilitate the type of research that this dataset is intended for. Publicly available deep-learning algorithm for performing this process is here: https://www.github.com/ecalabr/brain_mask/. Glossary of abbreviations: UCSF-PDGM-metadata_glossary.csv *Note: it was discovered that some ID are followup imaging of others, therefore the true number of patients in this Collection is 495 , the pixels have not been changed: UCSF-PDGM-0433 was imaged 7 days later as UCSF-PDGM-0315 (version 3 files reflect this change by renaming UCSF-PDGM-0315 to UCSF-PDGM-0433_FU007d) UCSF-PDGM-0431 was imaged 1 days later as UCSF-PDGM-0278 (version 3 files reflect this change by renaming UCSF-PDGM-0278 to UCSF-PDGM-0431_FU001d) UCSF-PDGM-0396 was imaged 175 days later as UCSF-PDGM-0175 (version 3 files reflect this change by renaming UCSF-PDGM-0175 to UCSF-PDGM-0396_FU175d) UCSF-PDGM-0429 was imaged 3 days later as UCSF-PDGM-0138 (version 3 files reflect this change by renaming UCSF-PDGM-0138 to UCSF-PDGM-0429_FU003d) UCSF-PDGM-0409 was imaged 1 days later as UCSF-PDGM-0181 (version 3 files reflect this change by renaming UCSF-PDGM-0181 to UCSF-PDGM-0409_FU001d) UCSF-PDGM-0391 was imaged 16 days later as UCSF-PDGM-0289 (version 3 files reflect this change by renaming UCSF-PDGM-0289 UCSF-PDGM-0391_FU016d) All image data have been "skull stripped", deidentified, pre-processed per the methods section of our abstract, and converted to NIfTI format. We cannot provide original DICOM data, however, these pre-processed files have been prepared to facilitate the type of research that this dataset is intended for. Publicly available deep-learning algorithm for performing this process is here: https://www.github.com/ecalabr/brain_mask/. Glossary of abbreviations: UCSF-PDGM-metadata_glossary.csv Term | Represents | Values |
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ID | DICOM (0010,0020) PatientID |
| Sex | DICOM (0010,0040) Patient Sex | M,F | Age at MRI | Age in years at time of MR imaging |
| WHO CNS Grade | Grade per the 2021 World Health Organization Classification of Tumors of the Central Nervous System (WHO CNS 2021) (https://doi.org/10.1093/neuonc/noab106 ) | 2,3,4 | Final pathologic diagnosis (WHO 2021) | Final (integrated) pathologic diagnosis per the 2021 World Health Organization Classification of Tumors of the Central Nervous System (WHO CNS 2021) | Term | Represents | Values |
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ID | DICOM (0010,0020) PatientID | Sex | DICOM (0010,0040) Patient Sex | M,F | Age at MRI | Age in years at time of MR imaging | WHO CNS Grade | Grade per the 2021 World Health Organization Classification of Tumors of the Central Nervous System (WHO CNS 2021) (https://doi.org/10.1093/neuonc/noab106 ) | 2,3,4 | Final pathologic diagnosis (WHO 2021) | Final (integrated) pathologic diagnosis per the 2021 World Health Organization Classification of Tumors of the Central Nervous System (WHO CNS 2021) ( https://doi.org/10.1093/neuonc/noab106 ) | - Glioblastoma, Isocitrate dehydrogenase (IDH) -wildtype,
- Astrocytoma, IDH-mutant,
- Astrocytoma, IDH-wildtype,
- Oligodendroglioma, IDH-mutant, 1p/19q-codeleted
| MGMT status | O6-methylguanine-DNA methyltransferase status - clinical interpretation of the MGMT index described below. | negative, positive, indeterminate | MGMT index | O6-methylguanine-DNA methyltransferase methylation index (in house method developed by UCSF clinical labs, https://genomics.ucsf.edu/content/mgmt-promoter-methylation-assay ) where numeric values 0-17 indicate the number of promoter methylation sites. | 0-17, blank | 1p/19q | presence of codeletion of 1p and 19q genes, assayed by fluorescent in-situ hybridization | intact, co-deletion, relative co-deletion, unknown | IDH | isocitrate dehydrogenase mutation subtype characterized with a capture-based targeted next-generation DNA sequencing panel (UCSF500) as described in ( https://doi.org/10.1093/neuonc/now254noab106 ) | 1-dead 0-alive | Survival status of the patient at last clinical follow up. | OS | Overall survival in days from initial diagnosis to last clinical follow up. | EOR | Extent of resection determined by review of operative reports and immediate postoperative imaging | biopsy (only biopsy) Subtotal resection (STR) gross total resection (GTR) | Biopsy prior to imaging | Was a burr-hole biopsy performed prior to imaging | yes, no, blank | - Glioblastoma, Isocitrate dehydrogenase (IDH) -wildtype,
- Astrocytoma, IDH-mutant,
- Astrocytoma, IDH-wildtype,
- Oligodendroglioma, IDH-mutant, 1p/19q-codeleted
| MGMT status | O6-methylguanine-DNA methyltransferase status - clinical interpretation of the MGMT index described below. | negative, positive, indeterminate | MGMT index | O6-methylguanine-DNA methyltransferase methylation index (in house method developed by UCSF clinical labs, https://genomics.ucsf.edu/content/mgmt-promoter-methylation-assay ) where numeric values 0-17 indicate the number of promoter methylation sites. | 0-17, blank | 1p/19q | presence of codeletion of 1p and 19q genes, assayed by fluorescent in-situ hybridization | intact, co-deletion, relative co-deletion, unknown | IDH | isocitrate dehydrogenase mutation subtype characterized with a capture-based targeted next-generation DNA sequencing panel (UCSF500) as described in (https://doi.org/10.1093/neuonc/now254 ) |
| 1-dead 0-alive | Survival status of the patient at last clinical follow up. |
| OS | Overall survival in days from initial diagnosis to last clinical follow up. |
| EOR | Extent of resection determined by review of operative reports and immediate postoperative imaging | biopsy (only biopsy) Subtotal resection (STR) gross total resection (GTR) | Biopsy prior to imaging | Was a burr-hole biopsy performed prior to imaging | yes, no, blank |
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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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| 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 |
| Localtab |
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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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| 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 2) [Dataset]. The Cancer Imaging Archive. DOI: 10.7937/tcia.bdgf-8v37 |
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title | Publication Citation |
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| Evan Calabrese, Javier E. Villanueva-Meyer, Jeffrey D. Rudie, Andreas M. Rauschecker, Ujjwal Baid, Spyridon Bakas, Soonmee Cha, John T. Mongan, Christopher P. Hess. The UCSF Preoperative Diffuse Glioma MRI (UCSF-PDGM) (Version 3) [Dataset. Radiology: Artificial Intelligence. DOI: https://doi.org/10.1148/ryai.220058 (in press)]. The Cancer Imaging Archive. DOI: 10.7937/tcia.bdgf-8v37 |
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title | TCIA Publication Citation |
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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. 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: 10.1007/s10278-013-9622-7 |
Other Publications Using This DataCalabrese E, Rudie JD, Rauschecker AM, Villanueva-Meyer JE, Cha S. Feasibility of Simulated Postcontrast MRI of Glioblastomas and Lower Grade Gliomas Using 3D Fully Convolutional Neural Networks. Radiology: Artificial Intelligence. 2021 May 19;e200276. - Calabrese E, Villanueva-Meyer JE, Cha S. A fully automated artificial intelligence method for non-invasive, imaging-based identification of genetic alterations in glioblastomas. Scientific Reports. 2020 Jul 16;10(1):11852.
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. Evan Calabrese, Javier E. Villanueva-Meyer, Jeffrey D. Rudie, Andreas M. Rauschecker, Ujjwal Baid, Spyridon Bakas, Soonmee Cha, John T. Mongan, Christopher P. Hess. The UCSF Preoperative Diffuse Glioma MRI (UCSF-PDGM) Dataset. Radiology: Artificial Intelligence. DOI: https://doi.org/10.1148/ryai.220058 (in press) |
Info |
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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. 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: 10.1007/s10278-013-9622-7 |
Other Publications Using This DataCalabrese E, Rudie JD, Rauschecker AM, Villanueva-Meyer JE, Cha S. Feasibility of Simulated Postcontrast MRI of Glioblastomas and Lower Grade Gliomas Using 3D Fully Convolutional Neural Networks. Radiology: Artificial Intelligence. 2021 May 19;e200276. - Calabrese E, Villanueva-Meyer JE, Cha S. A fully automated artificial intelligence method for non-invasive, imaging-based identification of genetic alterations in glioblastomas. Scientific Reports. 2020 Jul 16;10(1):11852.
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 |
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| Version 3 (Current): Updated 2023/01/11Data Type | Download all or Query/Filter | License |
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Images and Annotations (NIfTI format , 156 GB) |
Tcia button generator |
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url | https://faspex.cancerimagingarchive.net/aspera/faspex/external_deliveries/357?passcode=e722861fdd0278611166a64f0b66e46d9e6ae17c |
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| v3 Download |
(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) | | Clinical data (CSV)
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Tcia button generator |
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url | https://wiki.cancerimagingarchive.net/download/attachments/119705830/UCSF-PDGM-metadata_v2.csv?api=v2 |
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*Note: it was discovered that some ID are followup imaging of others, therefore the true number of patients in this Collection is 495, the pixels have not been changed: UCSF-PDGM-0433 was imaged 7 days later as UCSF-PDGM-0315 (version 3 files reflect this change by renaming UCSF-PDGM-0315 to UCSF-PDGM-0433_FU007d) UCSF-PDGM-0431 was imaged 1 day later as UCSF-PDGM-0278 (version 3 files reflect this change by renaming UCSF-PDGM-0278 to UCSF-PDGM-0431_FU001d) UCSF-PDGM-0396 was imaged 175 days later as UCSF-PDGM-0175 (version 3 files reflect this change by renaming UCSF-PDGM-0175 to UCSF-PDGM-0396_FU175d) UCSF-PDGM-0429 was imaged 3 days later as UCSF-PDGM-0138 (version 3 files reflect this change by renaming UCSF-PDGM-0138 to UCSF-PDGM-0429_FU003d) UCSF-PDGM-0409 was imaged 1 day later as UCSF-PDGM-0181 (version 3 files reflect this change by renaming UCSF-PDGM-0181 to UCSF-PDGM-0409_FU001d) UCSF-PDGM-0391 was imaged 16 days later as UCSF-PDGM-0289 (version 3 files reflect this change by renaming UCSF-PDGM-0289 UCSF-PDGM-0391_FU016d) Version 2: Updated 2022/11/30: | Localtab |
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| Version 2 (Current): Updated 2022/11/30Data Type | Download all or Query/Filter | License |
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Images and Annotations (NIfTI format , 156 GB) |
Tcia button generator |
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url | https://faspex.cancerimagingarchive.net/aspera/faspex/external_deliveries/355?passcode=74fa8e9291ff65e220c994599c6db0c7582f475d |
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(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) | | Clinical data (CSV)
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Tcia button generator |
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url | https://wiki.cancerimagingarchive.net/download/attachments/119705830/UCSF-PDGM-metadata_v2.csv?api=v2 |
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Changes to this version: - Fixes to integer rounding errors in *tumor_segmentation.nii.gz files by the Collection's investigators.
- TCIA users have asked for a mapping to the 2021 BraTS data to prevent any data leak when both datasets are used. Updated metadata spreadsheet attached which includes the BraTS IDs for all relevant cases. This data was confirmed by BraTS Challenge organizers.
- Correction of name suffix for bias corrected T1 postcontrast images from "T1gad_bias" to "T1c_bias" for consistency.
Version 1: Updated 2022/09/26Data Type | Download all or Query/Filter | License |
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Images and Annotations (NIfTI zip, 156 GB) |
Tcia button generator |
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url | https://faspex.cancerimagingarchive.net/aspera/faspex/external_deliveries/333?passcode=492e0b4256ec1b978f5c980960c156c3baad9d21# |
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(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) | | Clinical data (CSV) |
Tcia button generator |
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url | https://wiki.cancerimagingarchive.net/download/attachments/119705830/UCSF-PDGM-metadata.csv?api=v2 |
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