Phantom: DICOM Anonymization in Python

[cyrilzakka]

Hello everyone! I'm a medical doctor working at the intersection of machine learning and medicine.

I made a WIP DICOM anonymization tool in Python based on pydicom for my ML workflow. Unlike other anonymization modules, Phantom is whitelist-based, so anything not specified in the configuration file gets automatically purged from the metadata.

Phantom also partially supports getting rid of burned annotations in dynamic imaging modalities such as echocardiograms by masking any static pixels.

Looking forward to your feedback and tips!

Link: https://github.com/cyrilzakka/Phantom

[mrbean-bremen]

@vsoch - maybe you can give some feedback here, given your experience with deid...

[vsoch]

deid can target all with ALL by default and then KEEP particular ones, so what you are describing sounds like it might be a bug or you didn't read the full documentation / find an example that helped? Could you maybe open an issue and share something to reproduce?

We also have jitter and UID generation... maybe you just missed that. We support image cleaning for any annotations that are found where they are expected for different machine types based on CTP.

[cyrilzakka]

@vsoch oh I did miss the ‘ALL’ by default, my bad! And was just listing our 2 extra features, not arguing deid was missing them, so I apologize if it came off that way!

In my specific case, despite specifying REMOVE for attributes such as PatientsSex, PatientWeight, PatientTelephoneNumber etc. ‘deid’ seemed to miss them for my dataset after a few tries.

[vsoch]

You might have had a typo? There is no PatientsSex but there is PatientSex https://dicom.innolitics.com/ciods/general-ecg/patient/00100040. I don't have your recipe in front of me but I suspect there were maybe some issues.

Totally cool (and fun) to make your own tool! But please next time if something seems missing / off, open an issue because I wouldn't know you needed help otherwise.

[cyrilzakka]

@vsoch thank you for your time and feedback!

[vsoch]

Sure! If you ever try deid again please open an issue so I can help. It’s really on me to provide docs/examples to show different use cases, and it’s my failure if you didn’t find what you needed when you were trying to use it. Happy Friday!