pet-linear TypeError: unexpected keyword argument

[Andrina Arnold]

Dear Clinica users, 

I am struggling using the pet-linear pipeline and always get the following TypeError: TypeError: cli() got an unexpected keyword argument 'reconstruction'

Here is a more detailed description of my error:

clinica run pet-linear /Users/andrina/Desktop/BIDS_test/ /Users/andrina/Desktop/CAPS_test/ 18FAV1451 pons

Traceback (most recent call last):

  File "/Users/andrina/anaconda3/envs/clinicaEnv/bin/clinica", line 8, in <module>

    sys.exit(main())

  File "/Users/andrina/anaconda3/envs/clinicaEnv/lib/python3.8/site-packages/clinica/cmdline.py", line 92, in main

    cli()

  File "/Users/andrina/anaconda3/envs/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 1157, in __call__

    return self.main(*args, **kwargs)

  File "/Users/andrina/anaconda3/envs/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 1078, in main

    rv = self.invoke(ctx)

  File "/Users/andrina/anaconda3/envs/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 1688, in invoke

    return _process_result(sub_ctx.command.invoke(sub_ctx))

  File "/Users/andrina/anaconda3/envs/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 1688, in invoke

    return _process_result(sub_ctx.command.invoke(sub_ctx))

  File "/Users/andrina/anaconda3/envs/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 1434, in invoke

    return ctx.invoke(self.callback, **ctx.params)

  File "/Users/andrina/anaconda3/envs/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 783, in invoke

    return __callback(*args, **kwargs)

TypeError: cli() got an unexpected keyword argument 'reconstruction'

Does anybody know how to resolve this error?

Thank you very much for your help!

[Andrina Arnold]

I am using python 3.8 and clinica 0.7.6. version

[Nicolas Gensollen]

Hi Andrina,

Thanks for bringing this issue to our attention. Indeed, there seems to be an issue with the pet-linear command in version 0.7.6 of Clinica.

I will open an issue and look for a fix. In the mean time, you can use Clinica 0.7.5 to run your pipeline (unless you explicitly need to use the "reconstruction_method" argument but it doesn't seem to be the case from your screenshot).

You can run "pip install clinica==0.7.5" in a fresh environnement for example.

Let us know if you still encounter issues with the 0.7.5 version.

Best,

Nicolas