5ttgen hsvs error

1

Hi to all

While trying to run “5ttgen hsvs ${SUBJECTS_DIR}/subject_01 5tt.mif”, I am receiving error message:

“Error: argument algorithm: invalid choice: ‘hsvs’ (choose from ‘freesurfer’, ‘fsl’, ‘gif’)”

I am using the laters mrtrix version 3.0.8.

Thank you in advance.

Nabi

2

Hi Nabi,

I don’t immediately see any plausible way in which version 3.0.8 could yield that result without some form of user intervention.
Either:

  • You are in fact not invoking version 3.0.8 of the software as you believe you are
    (check output of which 5ttgen and 5ttgen -version)
  • 5ttgen from version 3.0.8 is checking for source code files in a location other than where the source code from version 3.0.8 is stored
    (check eg. whether you have set PYTHONPATH to point to an older version of MRtrix3)
  • You have compiled from source but have local modifications that include the deletion of file lib/mrtrix3/_5ttgen/hsvs.py

If those don’t identify the issue, could you please also let us know the environment that you are using (eg. OS, compiled from source vs. something like Conda)

Thanks
Rob