bilgelm / dynamicpet Goto Github PK

petbids concatenation should pay attention to decay correction info when concatenating.

Hello! Thank you for sharing this tool.

I am trying to run the kinfitr implementations, but having some trouble.

I've followed the instructions on the site and successfully loaded the kinfitr extra. I've also double checked the package is installed in R.
I am using ubuntu 22.04, python 3.11 and R 4.1.2, and the latest project commit.

I tried the following command:
kineticmodel sub-000101_ses-baseline_pet.nii.gz --model kinfitr.SRTM --refmask refmask_inPET.nii.gz --outputdir output --json sub-000101_ses-baseline_pet.json --fwhm 5

The command runs for about 15 seconds and then stops without error. However, when I check the output directory, there are no files. his happens with both available kinfitr models. This does not happen when I use the other models (e.g. SRTMZhou2003), where files are outputted correctly, so I can only assume there is a problem somewhere with kinfitr.

It is difficult to know without a log file but how can I tell if there is an issue with my own setup of the repository, or perhaps a bug somewhere in the code itself?

I'd greatly appreciate your insights on this! Thank you

This import should be done only if the user has specified a kinfitr method for kineticmodel. Without an R install, the import fails.

It might make sense to put R-dependent stuff (rpy2, kinfitr) into an extra.