DICOM-LIDC-IDRI-Nodules | Standardized representation of the TCIA LIDC-IDRI annotations using DICOM
DOI: 10.7937/TCIA.2018.h7umfurq | Data Citation Required | Analysis Result
| Location | Subjects | Size | Updated | |||
|---|---|---|---|---|---|---|
| Lung | Chest | 875 | Tumor segmentations, image features, Software/Source Code | 2020/03/26 |
Summary
This dataset contains standardized DICOM representation of the annotations and characterizations collected by the LIDC/IDRI initiative, originally stored in XML and available in the TCIA LIDC-IDRI collection . Only the nodules that were deemed to be greater or equal to 3 mm in the largest planar dimensions have been annotated and characterized by the expert radiologists performing the annotations. Only those nodules are included in the present dataset.
Conversion was enabled by the pylidc library (https://pylidc.github.io/) (parsing of XML, volumetric reconstruction of the nodule annotations, clustering of the annotations belonging to the same nodule, calculation of the volume, surface area and largest diameter of the nodules) and the dcmqi library (https://github.com/qiicr/dcmqi) (storing of the annotations into DICOM Segmentation objects, and storing of the characterizations and measurements into DICOM Structured Reporting objects). The script used for the conversion is available at https://github.com/qiicr/lidc2dicom. The details on the process of the conversion and the usage of the resulting objects are available in the citation (see Citations & Data Usage Policy section).
Data Access
Version 3: Updated 2020/03/26
What changed:
DICOM objects curated and added to the cancerimagingarchive.net
| Title | Data Type | Format | Access Points | Subjects | License | |||
|---|---|---|---|---|---|---|---|---|
| Structured Reports and Segmentations | SEG, SR | DICOM | Download requires NBIA Data Retriever |
875 | 883 | 13,718 | 13,718 | CC BY 3.0 |
| DSO Key | CSV | CC BY 3.0 |
Additional Resources For This Dataset
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.
- pylidc library (https://pylidc.github.io/)
- dcmqi library (https://github.com/qiicr/dcmqi)
- The script used for the conversion is available at https://github.com/qiicr/lidc2dicom
Citations & Data Usage Policy
Data Citation Required: Users must abide by the TCIA Data Usage Policy and Restrictions. Attribution must include the following citation, including the Digital Object Identifier:
Data Citation |
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Fedorov, A., Hancock, M., Clunie, D., Brockhhausen, M., Bona, J., Kirby, J., Freymann, J., Aerts, H.J.W.L., Kikinis, R., Prior, F. (2018). Standardized representation of the TCIA LIDC-IDRI annotations using DICOM. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.2018.h7umfurq |
Additional Publications Related To This Work
The Collection authors suggest the below will give context to this dataset:
- In addition to the dataset citation above, please be sure to cite the following if you utilize these data in your research:
- Armato SG III, et al.: The Lung Image Database Consortium (LIDC) and Image Database Resource Initiative (IDRI): A completed reference database of lung nodules on CT scans. Medical Physics, 38: 915–931, 2011. DOI: https://doi.org/10.1118/1.3528204
- Armato III, S. G., McLennan, G., Bidaut, L., McNitt-Gray, M. F., Meyer, C. R., Reeves, A. P., Zhao, B., Aberle, D. R., Henschke, C. I., Hoffman, E. A., Kazerooni, E. A., MacMahon, H., Van Beek, E. J. R., Yankelevitz, D., Biancardi, A. M., Bland, P. H., Brown, M. S., Engelmann, R. M., Laderach, G. E., Max, D., Pais, R. C. , Qing, D. P. Y. , Roberts, R. Y., Smith, A. R., Starkey, A., Batra, P., Caligiuri, P., Farooqi, A., Gladish, G. W., Jude, C. M., Munden, R. F., Petkovska, I., Quint, L. E., Schwartz, L. H., Sundaram, B., Dodd, L. E., Fenimore, C., Gur, D., Petrick, N., Freymann, J., Kirby, J., Hughes, B., Casteele, A. V., Gupte, S., Sallam, M., Heath, M. D., Kuhn, M. H., Dharaiya, E., Burns, R., Fryd, D. S., Salganicoff, M., Anand, V., Shreter, U., Vastagh, S., Croft, B. Y., Clarke, L. P. (2015). Data From LIDC-IDRI [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2015.LO9QL9SX
Publications Using This Data
TCIA maintains a list of publications which leverage our data. If you have a manuscript you’d like to add please contact TCIA’s Helpdesk.
Publication Citation |
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Fedorov, A., Hancock, M., Clunie, D., Brochhausen, M., Bona, J., Kirby, J., Freymann, J, Pieper S, Aerts H.J.W.L., Kikinis, R., Prior, F. (2020) DICOM re‐encoding of volumetrically annotated Lung Imaging Database Consortium (LIDC) nodules. Medical Physics Dataset Article. https://doi.org/10.1002/mp.14445 |
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., 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 |
Previous Versions
Version 2: Updated 2019/05/14
What changed: DICOM SEG objects no longer encode empty slices to reduce object size. The coded terms used to describe the nodule annotations now use fewer non-standard (99QIICR) codes. SegmentLabel attribute is populated in the DICOM SEG objects to list nodule annotation name instead of “Nodule”, to help with readability
for the user.
| Title | Data Type | Format | Access Points | Subjects | License | |||
|---|---|---|---|---|---|---|---|---|
| Structured Reports and Segmentations | SR | DICOM |
Version 1: Updated 2018/11/30
Note: Version 1 of this dataset is currently located in a shared Google Drive folder while undergoing verification. When testing is complete the Google Drive folder will be replaced by a different link to the final dataset.