Hello, I downloaded the imaging data from the Anti-PD-1 _ Lung collection in the TCIA database, however I did not find the clinical information of the patient, can you share how we get this clinical information and correlate its images? Thank you!
Anti-PD-1_Lung collection in IDC is ingested from TCIA. For the sake of completeness, to download this collection from IDC you would need to first install idc-index package, which you can do with the command below (assuming you have python and pip set up on your system):
pip install --upgrade idc-index
To download the content of this collection, you can run the following in the command line:
idc download anti_pd_1_lung
To check availability of clinical data for this collection you can again use idc-index package:
from idc_index import IDCClient
c = IDCClient()
# install component of the package with the metadata about available clinical data
c.fetch_index('clinical_index')
# select attributes available for the anti_pd_1_lung collection
nlst_clinical_data_columns = c.clinical_index[c.clinical_index['collection_id']=='anti_pd_1_lung']
nlst_clinical_data_columns[['short_table_name','column','column_label','values']]
The output of the above is the following (only the first few rows shown, due to large number of rows)
In this case, attributes available in the clinical data correspond to the assessments by the radiologists performed for the segmentations available for the anti_pd_1_lung collection in the BAMF-AIMI-Annotations analysis results collection: https://portal.imaging.datacommons.cancer.gov/explore/filters/?analysis_results_id=BAMF-AIMI-Annotations&collection_id=anti_pd_1_lung.
Checking the Anti-PD-1_Lung collection page in TCIA confirms that it does not have any clinical information accompanying the images. As demonstrated above, with IDC you can easily check availability of clinical data with few lines of code, and you can access it directly - when available - without downloading or parsing any files from the TCIA wiki pages. You can see a tutorial of how to search clinical data on the example of the NLST collection here: IDC-Tutorials/notebooks/collections_demos/nlst_clinical_data.ipynb at master · ImagingDataCommons/IDC-Tutorials · GitHub.
As a side note, it is curious how TCIA accepted the Anti-PD-1_Lung collection, which “[…] includes 46 lung cases treated with anti-PD1 immunotherapy in 2016, each with pre-treatment and most with 1 imaging follow-up timepoint” without requiring submitters to provide any clinical data about the studied cohort. You would need to reach out to TCIA to ask this question.
Thank you for your reply. I will download its clinical data according to the method you shared. In addition, I have also paid attention to the IDC usage notes you shared, and I will also learn these. To increase understanding of IDC. Thank you again for sharing.
Also, in your reply, In this case, attributes available in the clinical data correpond to the assessments by the radiologists performed for the segmentations available for the collection in the analysis results collection: https://portal.imaging.datacommons.cancer.gov/explore/filters/? Analysis _ results _ id = BAMF-AIMI-Annotations & collection _ id = anti _ pd _ 1 _ lung.anti _ pd _ 1 _ lungBAMF-AIMI-Annotations, I did not understand its meaning, the clinical data I downloaded according to your method only has some information of segmented CT images, and there is no age, gender, A series of basic clinical information about treatment response, how should I find them？
@Bright I am sorry for the confusion. I did not communicate it clearly. There is no clinical data associated with the images for this collection.
You can use the instructions to check availability of clinical data for any collection in IDC, but unfortunately it will not help you in the case of this specific collection.
Thank you very much for your help. Although I could not find the clinical information of these patients in IDC, I did see the table of its clinical information in relevant papers, but unfortunately it was not published. I really need this batch of data, based on your experience, what other ways do you think I can find its clinical data?
I recommend you contact both the corresponding author on the paper, and TCIA helpdesk, since TCIA ingested and curated this dataset from the submitter. Even if TCIA cannot locate the information you need, they will at least be aware that users need the accompanying information, and may take this into consideration for the next dataset they ingest.
Thank you for your response. If permitted, could you provide the contact information (email) of the creator of the Anti-PD-1 _ Lung collection dataset? Alternatively, could you guide me on how to obtain information related to the treatment responses of these patients? Since this dataset is about patients receiving immunotherapy, there should be annotations regarding their responses after treatment, correct?
I do not have any of that information.
The best I can recommend is contacting TCIA Helpdesk.