Practice (~60-minutes)
⛅️ Google Cloud Shell Tutorial
In this anonymization tutorial, you'll use gdcm and facemasking tools. After logging in to Google Cloud Shell, run the following command to retrieve the tutorial:
</div> language-'></div>">After retrieving the tutorial, initialize it and follow the instructions:
<div class='oc-markdown-activatable oc-markdown-custom-container' data-value='```bash
teachme tutorial_dicom_anonymize.md
'>
Note
- This practice lesson has it all: Unix command line, data downloads, a bin directory in your path for binaries and scripts, and running a container. If you have the prerequisite to this course (COGS 500), then this will all be familiar.
- If you have not used Google Cloud Shell before, you need to create an account and learn to use the interface.
- This is a significant detour (an hour or so) to get it set up (instructions are included when you get to the practice), and you may find some of this pretty opaque (even if you get through it).
- Consult the Google Cloud shell lesson.
- You should be able to complete the lesson after setting up an account and learning the interface. Let me know if you get stuck or feel lost, I can provide access to some background lessons.
- If you have not used Google Cloud Shell before, you need to create an account and learn to use the interface.
- This is a significant detour (an hour or so) to get it set up (instructions are included when you get to the practice), and you may find some of this pretty opaque (even if you get through it).
- Consult the Google Cloud shell lesson.
- You should be able to complete the lesson after setting up an account and learning the interface. Let me know if you get stuck or feel lost, I can provide access to some background lessons.
Summary
Practical Experience working with DICOMS The lesson provided practice working at the command line (Google cloud shell), installing binary programs, and using a Docker container. In particular, you used software tools that view and edit DICOM data. As you may recall, you can get to this metadata with Mango, but your ability to make changes across many scans and identify particular information in the gigantic header is limited.
Note
In the normal course of running a research study, you will probably never have to anonymize the DICOM data directly! However, you may have to query the DICOM data to extract information that is not available in the protocol (for example, for ASL data).
TO DO Checklist
✅ Upload the script recording from the dicom_anonymize Cloud shell tutorial to the D2L dicom_anonymize assignment.
