Problem with Neurodebian toolkit on Ubuntu 22.10

I’ve been trying to get FMRIB’s FSL toolkit running on Ubuntu 22.10. The downloaded fslinstaller.py runs absolutely fine without any errors, and clears both stages. It selects /usr/local/fsl as the default install directory. However, when trying to use FSL it is not detected. For instance, echo $FSLDIR returns nothing.I mean it literally returns an empty line. Anything else, including flirt -versio n and fsleyes simply returns a “not installed” message.

I was worried that may be the shell setup did not go properly, so I edited the ~/.bash_profile and added in the following. But unfortunately this didn’t work. If anyone has any suggestions, I will be grateful.

FSLDIR=/usr/local/fsl
. ${FSLDIR}/etc/fslconf/fsl.sh
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH
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Did you relog your shell after setup? Is grep for FSLDIR in etc as what you added to your local bash profile may interfere with something added to the system wide login profile?

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That seems to have fixed it. But it seems like every time I quit the terminal, I have to redo the source ~./bash_profile command to get FSL up and running.

Thanks for the help, Wendell!

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