PET processing pipelines suggestions

Hi All,

I’m starting to work with PET imaging and wanted to know if there are some (preferably open source) processing pipelines that people recommend. I looked around, but couldn’t see too much. Specifically I’m looking at generating SUVR values from FDG, Amyloid, and Tau PET. If it’s in python and Nipype even better!


Hi Alex!
I started working with PET and Im having trouble finding documentation on how to get SUVRs and time activity curve and etc. What did you use to pre process yours? Do you have any good documentation? I’m a beginner here so any/all details you can give me are much welcome :pray::slightly_smiling_face:

Hi Carolina,

My work has taken a brief detour, however when I looked I didn’t find much in the way of open source code bases. We’ll likely resort to writing a pipeline ourselves. However, let me know if you do find something that works well for you!


Hi to both of you!

The pipeline will (strongly) depend on the pet modality.
The most common software to process PET data is SPM (matlab based), eventhough the basic steps can be easly done with Freesurfer/FSL/ANTS. There are several tutorials online with the basic steps!

To compute the SUVr, you would need (preferably) a structural MRI, to get the anatomical localization of the region to normalize. The region to normalize will depend, again, on the tracer. Check this ref from my group with the corresponding reference regions for amyloid pet (
If you would like a more detailed step-by-step, just ask for it!

BONUS: if you need to reconstruct your pet data, take a look to: Corrections for quantitative PET — NiftyPET 2.0.0 documentation

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Hi slieped,

Thank you for the info. I feel pretty comfortable with the registration between PET and T1, as well as normalizing to get SUVR. It’s calculating SUV/correcting for the radioactive decay that I’m looking for a package on.

Thanks for the link to NiftyPET. I looked into NiftyPET, but it looks to me like it made for a PET/CT imaging. If it can be used for just PET processing I’d love to see an example!

Thanks again for the reply,

Hello Carolina please did you find anything in the subject I’m working on pet mri data and I need some help if possible, thank you very much

Hello, please is there any chnace to provide me a detailed step by step for pet mri quentification.
thank you in advance