openneuropet / PET2BIDS

PET2BIDS helps you convert your PET data into BIDS! raw PET scanner files (e.g. ecat, dicom) and additional side files like .e.g excel sheets -- paper @JOSS https://doi.org/10.21105/joss.06067
https://pet2bids.readthedocs.io
MIT License
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Update JHU and Canon phantom conversions #281

Closed bilgelm closed 3 months ago

bilgelm commented 6 months ago

Made updates to *_conversions.* for JHU and Canon metadata. Added "3D Reprojection" to PET_reconstruction_methods.json.

Notes:


📚 Documentation preview 📚: https://pet2bids--281.org.readthedocs.build/en/281/

bendhouseart commented 6 months ago

ecat2bids doesn’t respect user specified InjectedRadioactivityUnits of "mCi" and overrides it as “MBq”. (Similar issue with SpecificRadioactivityUnits.) Tried to figure out why this was happening, but was unsuccessful (this issue doesn’t happen with dcm2niix4pet). So my Siemens HRRT json generated with python_conversions.py is incorrect, but the kwargs values in the .py are correct.

It's a tricky dance as we want to respect what the user provides while also getting some of the units/conversions right. But as to why ecat2bids differs from dcm2niix4pet in this manner is most likely due to an implementation error on my part.

I'm also a bit confused as to why the phantoms ci isn't running on this PR....will clone and run make testphantoms and if all is hunky dory merge and close this PR.