Summary
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Acknowledgements
We would like to acknowledge the individuals and institutions that have provided data for this collection:
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Hospital/Institution Name city, state, country - Special thanks to First Last Names, degree PhD, MD, etc from the Department of xxxxxx, Additional Names from same location.
This dataset contains image annotations derived from the NCI Clinical Trial "Radiation Therapy, Amifostine, and Chemotherapy in Treating Young Patients With Newly Diagnosed Nasopharyngeal Cancer (ARAR0331)”. This dataset was generated as part of a National Cancer Institute project to augment images from The Cancer Imaging Archive with annotations that will improve their value for cancer researchers and artificial intelligence experts. Annotation ProtocolFor each patient, all scans were reviewed to identify and annotate the clinically relevant time points and sequences/series. In a typical patient all available time points were annotated. The following annotation rules were followed: - PERCIST criteria was followed for PET imaging. Specifically, the lesions estimated to have the most elevated SUVmax were annotated.
- RECIST 1.1 was otherwise generally followed for MR and CT imaging. A maximum of 5 lesions were annotated per patient scan (timepoint); no more than 2 per organ. The same 5 lesions were annotated at each time point. Lymph nodes were annotated if >1 cm in short axis. Other lesions were annotated if >1 cm.
- Three-dimensional segmentations of lesions were created in the axial plane. If no axial plane was available, lesions were annotated in the coronal plane.
- MRIs were annotated using the T1-weighted axial post contrast sequence.
- Some lesions may cross multiple exams (ie. an MRI of the head and an MRI of the neck). The images portions on each exam were then annotated. If, however, the complete lesion was visualized on either a neck or head exam, then the other exam was not annotated to avoid redundancy.
- Lesions were labeled separately.
- The volume of each annotated lesion was calculated and reported in cubic centimeters [cc] in a dataset metadata report.
- A “negative” annotation was created for any exam without findings.
At each time point: Volume calculations were performed for each segmented structure. These calculations are provided in the Annotation Metadata CSV.- A seed point (kernel) was created for each segmented structure. The seed points for each segmentation are provided in a separate DICOM RTSTRUCT file.
- SNOMED-CT “Anatomic Region Sequence” and “Segmented Property Category Code Sequence” and codes were inserted for all segmented structures.
- “Tracking ID” and “Tracking UID” tags were inserted for each segmented structure to enable longitudinal lesion tracking.
- Imaging time point codes were inserted to help identify each annotation in the context of the clinical trial assessment protocol.
- “Clinical Trial Time Point ID” was used to encode time point type using one of the following strings as applicable: “pre-dose” or “post-chemotherapy”.
- Content Item in “Acquisition Context Sequence” was added containing "Time Point Type" using Concept Code Sequence (0040,A168) selected from:
- (255235001, SCT, “Pre-dose”)
- (719864002, SCT, "Post-cancer treatment monitoring")
- (719864002, SCT, "Post-cancer treatment monitoring")
- (719864002, SCT, "Post-cancer treatment monitoring")
- A spreadsheet containing key details about the annotations is available in the Data Access section below.
- A Jupyter notebook demonstrating how to use the NBIA Data Retriever Command-Line Interface application and the REST API to access these data can be found in the Additional Resources section below.
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title | Data Access |
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title | Data Access |
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| Data AccessNote to curators! This macro is for collections that are restricted due to facial reconstruction possibility. Note to curators! This macro is for collections that are restricted because of a PI's embargo request General restricted license access |
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Note to curators! Only use the appropriate macro for your collection above, or the text below in the case of NCTN trials. It will need to be tailored with the correct NCT#. This is a limited access data set. To request access please register an account on the NCTN Data Archive. After logging in, use the "Request Data" link in the left side menu. Follow the on screen instructions, and enter NCT00352534 when asked which trial you want to request. In step 2 of the Create Request form, be sure to select “Imaging Data Requested”. Please contact NCINCTNDataArchive@mail.nih.gov for any questions about access requests. Data Type | Download all or Query/Filter | License |
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Images, Segmentations, and Radiation Therapy Structures/Doses/Plans ARAR0331 Annotations - Segmentations, Seed Points, and Negative Findings Assessments (DICOM, X.XX .X GB) << latter two items only if DICOM SEG/RTSTRUCT/RTDOSE/PLAN exist >>
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(Download requires NBIA Data Retriever) | | ARAR0331 Annotation Metadata (CSV) |
restrictedlicense Nctn_with_collab license only |
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Nctn_no_collab license only |
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Tissue Slide Images (SVS | | Original ARAR0331 Images used to create Segmentations and Seed Points (DICOM, XX.X GB) | | Tcia button generator |
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| (Download requires NBIA Data Retriever) | Aspera plugin) Nctn_with_collab license only |
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nctn_no_collab-license-only |
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Clinical data (CSV | Original ARAR0331 Images used to create Negative Assessment reports (DICOM, XX.X GB) |
(Download requires NBIA Data Retriever) | Nctn_with_collab license only |
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nctn_no_collab-license-only |
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Click the Versions tab for more info about data releases. Additional Resources for this DatasetNote to curators! Use this any time you are linking to NCI's IDC/GDC/PDC resources. The links below are examples and will need to be tailored to point to the specific dataset (see parameters in URLS). Nci_crdc additional resources |
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Note to curators! The link below is an example for NCTN trials and will need to be tailored to the proper URL for the corresponding data on the NCTN Data Archive. Nctn additional resources |
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Note to curators! Below are examples for what to do with other external resources/links that don't fit into the above categories. 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. - Software / Code on Github
- Genomics data in DbGAP
- Genomics data in Gene Expression Omnibus
Third Party Analyses of this Dataset
Collections Used in this Third Party Analyses TCIA encourages the community to publish your analyses of our datasets. Below is a list of such third party analyses published using this Collection:the collections used in these analyses:
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title | Detailed Description |
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| Detailed DescriptionImage Statistics | Radiology Image Statistics | Pathology Image Statistics |
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<< Add any additional information that didn't fit or belong in the Summary section. >>
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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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| DOI goes here. Create using Datacite with information from Collection Approval form |
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title | Publication Citation |
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| We ask on the proposal form if they have ONE traditional publication they'd like users to cite. |
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| Required acknowledgements only (ex:The CPTAC program requests that publications using data from this program...). If they just want to thank someone, that goes in the Acknowledgement section underneath the Summary. |
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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 |
Other Publications Using This DataTCIA maintains a list of publications which leverage TCIA data. If you have a manuscript you'd like to add please contact the TCIA Helpdesk. |
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| Version X (Current): Updated yyyy/mm/ddData Type | Download all or Query/Filter | License |
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Images, Segmentations, and Radiation Therapy Structures/Doses/Plans (DICOM, XX.X GB) << latter two items only if DICOM SEG/RTSTRUCT/RTDOSE/PLAN exist >> |
(Download requires the NBIA Data Retriever) | Nctn_with_collab license only |
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Nctn_no_collab license only |
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| Tissue Slide Images (SVS, XX.X GB) | | Nctn_with_collab license only |
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Nctn_no_collab license only |
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| Clinical data (CSV) | | Nctn_with_collab license only |
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Nctn_no_collab license only |
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