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

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Comment: updated citation formats, added shortname, all underlying data is untouched.

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  Segmentation Labels and Radiomic Features for the Pre-operative Scans of the TCGA-GBM collection  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  TCGA-GBM  and  TCGA-LGG  datasets. 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.

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Localtab Group



Localtab
activetrue
titleData Access

Data Access

Click the Download  button to save a ".tcia" manifest file to your computer, which you must open with the  NBIA Data Retriever


Data TypeDownload all or Query/Filter
TCGA-LGG images - 65 subjects (DICOM, 17 GB)

TCGA-GBM images - 102 subjects (DICOM, 32 GB)

Segmentations -  (DICOM, 4 GB)

DCMQI Metadata (ZIP, 3.1 MB)

TCGA key mapping (CSV)


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:




Localtab
titleDetailed Description

Detailed Description


CollectionStatistics

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 

Public collection license

Info
titleData Citation

Andrew Beers, Elizabeth Gerstner, Bruce Rosen, David Clunie, Steve Pieper, Andrey Fedorov, Jayashree Kalpathy-CramerA., 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
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, Volume 26, Number 6 pp 1045-1057. DOI: (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
titlePublication Citation

Spyridon Bakas, S., Hamed Akbari, Aristeidis H., Sotiras, Michel Bilello, Michel Rozycki, Justin S Kirby, John B Freymann, Keyvan Farahani, Christos Davatzikos. "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", Nature . Scientific Data, 4:170117 doi: (1). https://doi.org/10.1038/sdata.2017.117 (2017). https://www.nature.com/articles/sdata2017117


Info
titleData Citation
Spyridon

Bakas,

Hamed

S., Akbari,

Aristeidis

H., Sotiras,

Michel

A., Bilello,

Martin Rozycki, Justin Kirby, John Freymann, Keyvan Farahani, and Christos Davatzikos

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-LGG collection[Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2017.GJQ7R0EF


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 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 the TCIA Helpdesk.




Localtab
titleVersions

Version 1 (Current): 2020/04/30


Data TypeDownload all or Query/Filter
TCGA-LGG images - 65 subjects (DICOM, 17 GB)

TCGA-GBM images - 102 subjects (DICOM, 32 GB)

Segmentations -  (DICOM, 4 GB)

DCMQI Metadata (ZIP, 3.1 MB)

TCGA key mapping (CSV)





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