Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update JHU and Canon phantom conversions #281

Merged
merged 5 commits into from
Jun 4, 2024
Merged

Conversation

bilgelm
Copy link
Collaborator

@bilgelm bilgelm commented Mar 4, 2024

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

Notes:

  • 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.
  • Decided to use "3D Reprojection" rather than "3D Kinahan-Rogers", since the former seems to be more common in the literature.
  • Haven't tested/inspected the matlab conversions.

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

@bendhouseart
Copy link
Contributor

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.

@bendhouseart bendhouseart merged commit e49524e into main Jun 4, 2024
13 of 16 checks passed
@bendhouseart bendhouseart deleted the update-canon-phantoms branch June 4, 2024 22:30
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants