Score:1

FSL installs on Ubuntu 22.10, but no FSL function is available

fr flag

I tried installing FMRIB's FSL toolkit 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 -version and fsleyes simply returns a "not installed" message.

I couldn't find any record of this specific issue, so I figured asking here might help. If anybody has any ideas, you have my advanced gratitude.

Score:1
fr flag

Okay, so after a bit of poking around I figured out what the problem was. It appears that you have to relog the shell every time you close your terminal window.

I have to redo the source ~./bash_profile command to get FSL up and running every time.

EDIT (Jan, 8, 2023):

This issue of having to relog the shell after exiting terminal has disappeared on its own with the latest version of FSL. Simply download the new installer and update FSL.

Score:1
hk flag

On my computer, my FSLDIR is /usr/local/fsl. You could verify if it is the same for you and add

export FSLDIR=/usr/local/fsl

to your .bashrc or .bash_profile (supposing you're using linux).

See here. https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/ShellSetup

Sayantan Mandal avatar
fr flag
Yeah, the folder was always there, but I was still getting the error. Turns out, every time I close the terminal, I need to relog the shell again to get FSL up and running. Do you have to do this too?
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