As we discussed earlier, it would be great if we could include various notebooks that could help users get started with IDC. We should discuss what makes sense to include, and link those from the documentation. If you have ideas, or better ready to go notebooks that would make sense to share publicly with the users as is or with minimal changes, please respond to this thread with the details!
Here’s an example notebook with various ways of accessing the healthcare dicom store APIs:
Should this work? I logged into gcloud both as firstname.lastname@example.org and email@example.com, and logged in successfully. However, the cells below the login cell failed for both sets of credentials.
Hi Brad -
Sorry, I should have made it more clear - I’ll update the notebook to clarify.
To get access to the TCIA data via DICOMweb you need to fill out this form:
The reason is that Google doesn’t charge for egress on this data so they need to approve account on an individual basis. Usually it only takes a day or so turnaround.
Done. Yes it might be wise to add a comment like this to the notebook, as I am sure others will follow my (mis)steps
Sounds good - I did update the notebook intro text so I hope it’s clearer now.
Thanks @bje for trying things out!
Note that for the MVP release we will need to update that notebook to operate on the data stored by IDC, not by Google, so I expect the introduction will need to change again.
Also, see related post here: DICOMWeb access to hosted collections.
I put two first notebooks into this repo: https://github.com/ImagingDataCommons/IDC-Notebooks. One is about exploring metadata for the LIDC collection, and visualization of the content using IDC viewer, and the other one is about downloading a cohort.
@bje and anyone else interested who is not on the IDC team -it’s a private repo for now, but if you are interested, let me know your github login, and I can give you access.
p.s. Colab links for convenience:
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