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--- |
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license: cc-by-3.0 |
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tags: |
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- medical |
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viewer: false |
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--- |
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# The Cancer Genome Atlas Ovarian Cancer (NSCLC-Radiomics) |
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The models featured in this repository uses images from the publicly available [NSCLC-Radiomics](https://wiki.cancerimagingarchive.net/display/Public/NSCLC-Radiomics) Dataset. |
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Download the data from TCIA with **Classic Directory Name** download option. |
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## Converting Format |
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Convert DICOM images and segmentation to NIFTI format using SimpleITK, [pydicom](https://pydicom.github.io/) and [pydicom-seg](https://razorx89.github.io/pydicom-seg/guides/read.html). Run: |
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```shell |
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user@machine:~/NSCLC-Radiomics-NIFTI$ python convert.py |
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``` |
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## Segmentations |
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Images will have one of the following segmentation files: |
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``` |
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─ seg-Esophagus.nii.gz # 1 |
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─ seg-GTV-1.nii.gz # 2 |
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─ seg-Heart.nii.gz # 3 |
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─ seg-Lung-Left.nii.gz # 4 |
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─ seg-Lung-Right.nii.gz # 5 |
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─ seg-Spinal-Cord.nii.gz # 6 |
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``` |
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To combine segmentations into single nifti file, run `combine_segmentations.py`. |
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## Requirements |
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``` |
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pandas==1.5.0 |
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pydicom==2.3.1 |
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pydicom-seg==0.4.1 |
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SimpleITK==2.2.0 |
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tqdm==4.64.1 |
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``` |
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## Citation |
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If using this repository, please cite the following works: |
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``` |
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Data Citation |
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Aerts, H. J. W. L., Wee, L., Rios Velazquez, E., Leijenaar, R. T. H., Parmar, C., Grossmann, P., |
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Carvalho, S., Bussink, J., Monshouwer, R., Haibe-Kains, B., Rietveld, D., Hoebers, F., |
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Rietbergen, M. M., Leemans, C. R., Dekker, A., Quackenbush, J., Gillies, R. J., Lambin, P. (2019). |
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Data From NSCLC-Radiomics (version 4) [Data set]. |
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The Cancer Imaging Archive. |
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https://doi.org/10.7937/K9/TCIA.2015.PF0M9REI |
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Publication Citation |
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Aerts, H. J. W. L., Velazquez, E. R., Leijenaar, R. T. H., Parmar, C., Grossmann, P., Carvalho, S., |
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Bussink, J., Monshouwer, R., Haibe-Kains, B., Rietveld, D., Hoebers, F., Rietbergen, M. M., |
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Leemans, C. R., Dekker, A., Quackenbush, J., Gillies, R. J., Lambin, P. (2014, June 3). |
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Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach. |
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Nature Communications. Nature Publishing Group. |
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https://doi.org/10.1038/ncomms5006 (link) |
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TCIA 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, |
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Tarbox L, Prior F. |
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The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository, |
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Journal of Digital Imaging, Volume 26, Number 6, December, 2013, pp 1045-1057. |
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https://doi.org/10.1007/s10278-013-9622-7 |
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``` |
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