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  • DICOM-SEG Conversions for TCGA-LGG and TCGA-GBM Segmentation Datasets (DICOM-Glioma-SEG)

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Info
titleData Citation

Andrew Beers, Elizabeth Gerstner, Bruce Rosen, David Clunie, Steve Pieper, Andrey Fedorov, Jayashree Kalpathy-Cramer. (2017) DICOM-SEG Conversions for TCGA-LGG and TCGA-GBM Segmentation Datasets. The Cancer Imaging Archive. https://doi.org/

Description

This dataset contains DICOM-SEG (DSO) conversions of the  Segmentation Labels and Radiomic Features for the Pre-operative Scans of the TCGA-LGG collection and  and  Segmentation Labels and Radiomic Features for the Pre-operative Scans of the TCGA-GBM collection analysis  analysis datasets.
 
The MR volumes and segmentations provided in the original segmentation datasets (T1 pre-contrast, T1 post-contrast, T2, FLAIR) are in NIfTI format, co-registered to an atlas space, and re-sampled to 1mm isotropic resolution. This dataset contains DICOM-SEG versions of the same segmentations, transformed back into the original patient resolutions and orientations found in the TCIA’s TCIA’s TCGA-GBM and  and TCGA-LGG  datasetsdatasets. This allows users to extract features from MR sequences without introducing interpolation artifacts from isotropic resampling.
 
The process for creating these DSO objects is as follows. Patient data from the original NIfTI datasets were registered and resampled from isotropic space to patient space and resolution using  3DSlicer’s BRAINSFit module . The affine transformation files from these registrations are used to register and resample both the semi-automatic and automatic NIfTI segmentations into the spaces of each original MR DICOM dataset. These transformed NIfTI segmentations are then converted into DICOM-SEG datasets using the software package  dcmqi . Because each MR sequence has a unique patient space and resolution, the resulting dataset contains four DSO segmentations for each original NIfTI segmentation.
 

Included in this dataset are the converted DSO volumes, DSO metadata values used in the DSO conversion program dcmqi, and affine transformation files from isotropic space to the original patient space saved in ITK format. Original patient DICOM volumes are also available for download below. A key is provided that maps individual DSO objects to their corresponding DICOM Series UID, to facilitate easier data analysis.
 

Localtab Group



Localtab
activetrue
titleData Access

Data Access

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Be sure to "request dataset" with these : DICOM-Glioma-SEG, TCGA-GBM, and TCGA-LGG in your Agreement on page 1 so that we can process your request efficiently. Complete all pages.


Data Type

Please also cite the following original datasets and manuscript when citing this dataset:

Publication
Download all or Query/FilterLicense
Segmentations (DICOM, 4 GB)


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urlhttps://wiki.cancerimagingarchive.net/download/attachments/41517733/TCGA-GBM%20MR%20Images%20DICOM%20Seg%20Conversions%20NBIA-manifest%20April%202020.tcia?api=v2



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labelSearch
urlhttps://nbia.cancerimagingarchive.net/nbia-search/?CollectionCriteria=TCGA-GBM,TCGA-LGG?text-search=ow6ce3ml


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DCMQI Metadata (JSON , TXT, ZIP, 3.1 MB)


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urlhttps://wiki.cancerimagingarchive.net/download/attachments/41517733/TCGA_Segmentation%20DCMQI%20Metadata.zip?api=v2



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TCGA key mapping (CSV)


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urlhttps://wiki.cancerimagingarchive.net/download/attachments/41517733/TCGA_DSO_Key.csv?api=v2



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

Collections Used in this Third Party Analysis

Below is a list of the Collections used in these analyses:

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Data TypeDownload all or Query/FilterLicense

Corresponding Original MR Images from TCGA-LGG images 65 subjects (DICOM, MR, 17 GB)


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urlhttps://wiki.cancerimagingarchive.net/download/attachments/41517733/doiJNLP-JAMS4RFq.tcia?api=v2



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labelSearch
urlhttps://nbia.cancerimagingarchive.net/nbia-search/?ImageModalityCriteria=MR&MinNumberOfStudiesCriteria=1&PatientCriteria=TCGA-CS-4942,TCGA-CS-4944,TCGA-CS-5393,TCGA-CS-5396,TCGA-CS-5397,TCGA-CS-6186,TCGA-CS-6188,TCGA-CS-6665,TCGA-CS-6666,TCGA-CS-6668,TCGA-CS-6669,TCGA-DU-5851,TCGA-DU-5854,TCGA-DU-5855,TCGA-DU-5872,TCGA-DU-5874,TCGA-DU-6404,TCGA-DU-6542,TCGA-DU-7008,TCGA-DU-7010,TCGA-DU-7014,TCGA-DU-7015,TCGA-DU-7018,TCGA-DU-7019,TCGA-DU-7294,TCGA-DU-7298,TCGA-DU-7299,TCGA-DU-7300,TCGA-DU-7301,TCGA-DU-7302,TCGA-DU-7304,TCGA-DU-7306,TCGA-DU-7309,TCGA-DU-8162,TCGA-DU-8164,TCGA-DU-8166,TCGA-DU-8167,TCGA-DU-8168,TCGA-DU-A5TR,TCGA-DU-A5TS,TCGA-DU-A5TT,TCGA-DU-A5TU,TCGA-DU-A5TW,TCGA-DU-A5TY,TCGA-DU-A6S7,TCGA-DU-A6S8,TCGA-FG-5964,TCGA-FG-6689,TCGA-FG-6691,TCGA-FG-6692,TCGA-FG-7634,TCGA-FG-A4MT,TCGA-HT-7473,TCGA-HT-7602,TCGA-HT-7680,TCGA-HT-7686,TCGA-HT-7690,TCGA-HT-7694,TCGA-HT-7879,TCGA-HT-7884,TCGA-HT-8018,TCGA-HT-8111,TCGA-HT-8114,TCGA-HT-8563,TCGA-HT-A61A


(Download requires the NBIA Data Retriever and permission)

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Corresponding Original MR Images from TCGA-GBM images 102 subjects (DICOM, MR, 32 GB)


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urlhttps://wiki.cancerimagingarchive.net/download/attachments/41517733/doiJNLP-QoOaKUdn.tcia?api=v2




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labelSearch
urlhttps://nbia.cancerimagingarchive.net/nbia-search/?ImageModalityCriteria=MR&MinNumberOfStudiesCriteria=1&PatientCriteria=TCGA-02-0006,TCGA-02-0009,TCGA-02-0011,TCGA-02-0027,TCGA-02-0033,TCGA-02-0034,TCGA-02-0037,TCGA-02-0046,TCGA-02-0047,TCGA-02-0054,TCGA-02-0059,TCGA-02-0064,TCGA-02-0068,TCGA-02-0069,TCGA-02-0070,TCGA-02-0075,TCGA-02-0085,TCGA-02-0086,TCGA-02-0087,TCGA-02-0102,TCGA-02-0106,TCGA-02-0116,TCGA-06-0119,TCGA-06-0122,TCGA-06-0130,TCGA-06-0137,TCGA-06-0138,TCGA-06-0139,TCGA-06-0142,TCGA-06-0145,TCGA-06-0149,TCGA-06-0154,TCGA-06-0158,TCGA-06-0162,TCGA-06-0164,TCGA-06-0176,TCGA-06-0177,TCGA-06-0179,TCGA-06-0182,TCGA-06-0184,TCGA-06-0185,TCGA-06-0187,TCGA-06-0188,TCGA-06-0190,TCGA-06-0192,TCGA-06-0238,TCGA-06-0240,TCGA-06-0644,TCGA-06-0646,TCGA-06-1084,TCGA-06-1802,TCGA-06-2570,TCGA-06-5408,TCGA-06-5413,TCGA-06-5417,TCGA-06-6389,TCGA-08-0355,TCGA-08-0356,TCGA-08-0359,TCGA-08-0360,TCGA-08-0385,TCGA-08-0389,TCGA-08-0390,TCGA-08-0392,TCGA-08-0509,TCGA-08-0512,TCGA-08-0520,TCGA-08-0522,TCGA-12-0616,TCGA-12-0776,TCGA-12-0829,TCGA-12-1094,TCGA-12-1098,TCGA-12-1598,TCGA-12-1601,TCGA-12-3650,TCGA-14-1456,TCGA-14-1794,TCGA-14-1825,TCGA-14-3477,TCGA-19-0963,TCGA-19-1789,TCGA-19-2624,TCGA-19-2631,TCGA-19-5951,TCGA-19-5954,TCGA-19-5958,TCGA-19-5960,TCGA-76-4932,TCGA-76-4934,TCGA-76-4935,TCGA-76-6191,TCGA-76-6193,TCGA-76-6280,TCGA-76-6282,TCGA-76-6285,TCGA-76-6656,TCGA-76-6657,TCGA-76-6661,TCGA-76-6662,TCGA-76-6663,TCGA-76-6664


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Localtab
titleDetailed Description

Detailed Description


CollectionRadiology Imaging Statistics

Number of Studies

168*

Number of Series

1304

Number of Patients

167

Number of Images

1304

Modalities

SEG

Image Size (GB)4



*For TCGA-GBM patient TCGA-06-0192, there were 2 studies.




Localtab
titleCitations & Data Usage Policy

Citations & Data Usage Policy 

Tcia limited license policy


Info
titleData Citation

Beers, A., Gerstner, E., Rosen, B., Clunie, D., Pieper, S., Fedorov, A., & Kalpathy-Cramer, J. (2018). DICOM-SEG Conversions for TCGA-LGG and TCGA-GBM Segmentation Datasets [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.2018.ow6ce3ml



Info
titlePublication Citation

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. Scientific Data, 4(1)

Info
titleData Citation
Spyridon Bakas, Hamed Akbari, Aristeidis Sotiras, Michel Bilello, Martin Rozycki, Justin Kirby, John Freymann, Keyvan Farahani, and Christos Davatzikos. (2017) Segmentation Labels and Radiomic Features for the Pre-operative Scans of the TCGA-LGG collection. The Cancer Imaging Archive

. https://doi.org/10.

7937/K9/TCIA.2017.GJQ7R0EF

1038/sdata.2017.117 https://www.nature.com/articles/sdata2017117



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, 26(6), 1045–1057. https://doi.org/10.1007/s10278-013-9622-7



In addition to the dataset citation above, please be sure to cite the following if you utilize these data in your research:


Info
titleData Citation
Spyridon

Bakas,

Hamed Akbari, Aristeidis Sotiras, Michel Bilello, Martin Rozycki, Justin Kirby, John Freymann, Keyvan Farahani, and Christos Davatzikos

S., Akbari, H., Sotiras, A., Bilello, M., Rozycki, M., Kirby, J., Freymann, J., Farahani, K., & Davatzikos, C. (2017). Segmentation Labels

and Radiomic Features

for the Pre-operative Scans of the TCGA-

GBM

LGG collection [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2017.

KLXWJJ1Q

GJQ7R0EF


Info
title
Data Citation
Spyridon

Bakas,

Hamed

S., Akbari,

Aristeidis

H., Sotiras,

Michel Bilello, Michel Rozycki, Justin S Kirby, John B Freymann, Keyvan Farahani, Christos Davatzikos. "Advancing The Cancer Genome Atlas glioma MRI collections with expert segmentation labels and radiomic features", Nature Scientific Data, 4:170117 doi: 10.1038/sdata.2017.117 (2017).

Download

...

DICOM Segmentations, Registration Transformations, and DCMQI metadata

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


Other Publications Using This Data

TCIA maintains a list of publications that leverage TCIA data. If you have a manuscript you'd like to add please contact TCIA's Helpdesk.




Localtab
titleVersions

Version 1 (Current): 2020/04/30

Data TypeDownload all or Query/FilterLicense
Segmentations (DICOM, 4 GB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/41517733/TCGA-GBM%20MR%20Images%20DICOM%20Seg%20Conversions%20NBIA-manifest%20April%202020.tcia?api=v2



Tcia button generator
labelSearch
urlhttps://nbia.cancerimagingarchive.net/nbia-search/?CollectionCriteria=TCGA-GBM,TCGA-LGG?text-search=ow6ce3ml


(Download requires the NBIA Data Retriever and permission)

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DCMQI Metadata (JSON , TXT, ZIP, 3.1 MB)


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urlhttps://wiki.cancerimagingarchive.net/download/attachments/41517733/TCGA_Segmentation%20DCMQI%20Metadata.zip?api=v2



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TCGA key mapping (CSV)


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urlhttps://wiki.cancerimagingarchive.net/download/attachments/41517733/TCGA_DSO_Key.csv?api=v2



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Corresponding Original MR Images from TCGA-LGG images 65 subjects (DICOM, MR, 17 GB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/41517733/doiJNLP-JAMS4RFq.tcia?api=v2



Tcia button generator
labelSearch
urlhttps://nbia.cancerimagingarchive.net/nbia-search/?ImageModalityCriteria=MR&MinNumberOfStudiesCriteria=1&PatientCriteria=TCGA-CS-4942,TCGA-CS-4944,TCGA-CS-5393,TCGA-CS-5396,TCGA-CS-5397,TCGA-CS-6186,TCGA-CS-6188,TCGA-CS-6665,TCGA-CS-6666,TCGA-CS-6668,TCGA-CS-6669,TCGA-DU-5851,TCGA-DU-5854,TCGA-DU-5855,TCGA-DU-5872,TCGA-DU-5874,TCGA-DU-6404,TCGA-DU-6542,TCGA-DU-7008,TCGA-DU-7010,TCGA-DU-7014,TCGA-DU-7015,TCGA-DU-7018,TCGA-DU-7019,TCGA-DU-7294,TCGA-DU-7298,TCGA-DU-7299,TCGA-DU-7300,TCGA-DU-7301,TCGA-DU-7302,TCGA-DU-7304,TCGA-DU-7306,TCGA-DU-7309,TCGA-DU-8162,TCGA-DU-8164,TCGA-DU-8166,TCGA-DU-8167,TCGA-DU-8168,TCGA-DU-A5TR,TCGA-DU-A5TS,TCGA-DU-A5TT,TCGA-DU-A5TU,TCGA-DU-A5TW,TCGA-DU-A5TY,TCGA-DU-A6S7,TCGA-DU-A6S8,TCGA-FG-5964,TCGA-FG-6689,TCGA-FG-6691,TCGA-FG-6692,TCGA-FG-7634,TCGA-FG-A4MT,TCGA-HT-7473,TCGA-HT-7602,TCGA-HT-7680,TCGA-HT-7686,TCGA-HT-7690,TCGA-HT-7694,TCGA-HT-7879,TCGA-HT-7884,TCGA-HT-8018,TCGA-HT-8111,TCGA-HT-8114,TCGA-HT-8563,TCGA-HT-A61A


(Download requires the NBIA Data Retriever and permission)

Tcia restricted license

Corresponding Original MR Images from TCGA-GBM images 102 subjects (DICOM, MR, 32 GB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/41517733/doiJNLP-QoOaKUdn.tcia?api=v2




Tcia button generator
labelSearch
urlhttps://nbia.cancerimagingarchive.net/nbia-search/?ImageModalityCriteria=MR&MinNumberOfStudiesCriteria=1&PatientCriteria=TCGA-02-0006,TCGA-02-0009,TCGA-02-0011,TCGA-02-0027,TCGA-02-0033,TCGA-02-0034,TCGA-02-0037,TCGA-02-0046,TCGA-02-0047,TCGA-02-0054,TCGA-02-0059,TCGA-02-0064,TCGA-02-0068,TCGA-02-0069,TCGA-02-0070,TCGA-02-0075,TCGA-02-0085,TCGA-02-0086,TCGA-02-0087,TCGA-02-0102,TCGA-02-0106,TCGA-02-0116,TCGA-06-0119,TCGA-06-0122,TCGA-06-0130,TCGA-06-0137,TCGA-06-0138,TCGA-06-0139,TCGA-06-0142,TCGA-06-0145,TCGA-06-0149,TCGA-06-0154,TCGA-06-0158,TCGA-06-0162,TCGA-06-0164,TCGA-06-0176,TCGA-06-0177,TCGA-06-0179,TCGA-06-0182,TCGA-06-0184,TCGA-06-0185,TCGA-06-0187,TCGA-06-0188,TCGA-06-0190,TCGA-06-0192,TCGA-06-0238,TCGA-06-0240,TCGA-06-0644,TCGA-06-0646,TCGA-06-1084,TCGA-06-1802,TCGA-06-2570,TCGA-06-5408,TCGA-06-5413,TCGA-06-5417,TCGA-06-6389,TCGA-08-0355,TCGA-08-0356,TCGA-08-0359,TCGA-08-0360,TCGA-08-0385,TCGA-08-0389,TCGA-08-0390,TCGA-08-0392,TCGA-08-0509,TCGA-08-0512,TCGA-08-0520,TCGA-08-0522,TCGA-12-0616,TCGA-12-0776,TCGA-12-0829,TCGA-12-1094,TCGA-12-1098,TCGA-12-1598,TCGA-12-1601,TCGA-12-3650,TCGA-14-1456,TCGA-14-1794,TCGA-14-1825,TCGA-14-3477,TCGA-19-0963,TCGA-19-1789,TCGA-19-2624,TCGA-19-2631,TCGA-19-5951,TCGA-19-5954,TCGA-19-5958,TCGA-19-5960,TCGA-76-4932,TCGA-76-4934,TCGA-76-4935,TCGA-76-6191,TCGA-76-6193,TCGA-76-6280,TCGA-76-6282,TCGA-76-6285,TCGA-76-6656,TCGA-76-6657,TCGA-76-6661,TCGA-76-6662,TCGA-76-6663,TCGA-76-6664


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