In the Radiology Informatics Lab at Mayo Clinic (MN), we have been working on developing a couple of tutorial notebooks to work with IDC database. Like the previous tutorial notebooks my colleagues have already developed, I would like to share another notebook that I have been working on recently:
This repository includes a sample Google Cloud notebook that shows how to train a 3D classification model on Imaging Data Commons (IDC) buckets.
Here are what I have covered in this notebook:
- How to connect Google Cloud with IDC.
- How to retrieve the DICOMs metadata from IDC using BigQuery commands.
- How to download DICOMs from IDC.
- How to change DICOMs to NIFTIs in the clouds.
- How to pre-process data and train a 3D model on it using MONAI and Pytorch.
In case of any issues, please contact me in discourse or via this email address:
Hope you find it helpful!