Dear Lorenzo,

it could be that all that's missing is that your shell is not setup correctly, i.e., the FSL environment variables may not be set correctly and the FSL bin directory may not be part of your PATH.

1) Which shell are you using? I assume bash, the Ubuntu default shell?

2) Could you report the output of the following 2 commands:
-  echo $FSL_DIR
-  echo $PATH

I do not know about the neurodebian package, but if you installed from the python script and did not change the default location, your FSL installation should be in /usr/local/fsl/. In that case, you should be able to run flsmaths by typing:

  /usr/local/fsl/bin/fslmaths

(But you should definitely get the shell setup fixed.)

Best,

Tim

> On February 18, 2019 at 6:39 PM Lorenzo Mancuso <[log in to unmask]> wrote:
> 
> 
> Dear FSL experts,
> 
> I have installed FSL on Lubuntu 18.04 on an old 32 bit PC. It seems it could not been upgraded after v. 5.0.9, and it could not install FSLeyes. This is not a huge problem for me, as the use of this old computer is a temporary solution, however I encountered a weirder and more annoying issue: using any FSLUTILS such as fslmaths or fslmerge in the terminal, I always get a "command not found" error message. At the same time, GUI tools such as FLIRT or BET work flawlessly. I do not think that this could be related to the old version of FSL or to the architecture of my PC, so it is a particularly strange problem, and I am afraid that it could be related to some installation error that I could encounter it also in newer machines. Moreover, I would need to use fslmaths right now, and it would be nice to solve this problem. However, I already tried to re-install FSL from scratch, from both the neurodebian repository through apt-get and using the python script.
> 
> Anyone have some ideas on what is going wrong inside my computer? If you can provide me a solution it would be nice, but even if no solution are possible, any explanantion or hypothesis that could give me further understanding on how FSL works it will be appreciated. Should I post this message on the neurodebian mailing list?
> 
> Thank you in advance
> 
> Lorenzo Mancuso
> 
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-- 
Tim

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