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pauldmccarthy / fsleyes

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https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/
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Can open FSLeyes from terminal, but no icon is seen in utilities (macOS Monterey) #96

Closed JohannaHeu closed 2 years ago

JohannaHeu commented 2 years ago

Hi :)

I have a problem. I installed FSL on my Mac including XQuartz. Everything is working fine from the terminal. But there is one problem: I cannot see the icon FSLeyes in my Utilities folder. Moreover, when I open FSLeyes from the terminal (which is working fine) the icon is named "python" and not "FSLeyes".

When I search it on my Mac FSLeyes is saved in a folder called "fslpython". When I move the application from this folder manually to applications, I am not able to open as there is an error saying: file incomplete or damaged

Is there maybe a trick so I can see the icon in my applications too?

Thanks a lot! Greetings Johanna

pauldmccarthy commented 2 years ago

Hi @JohannaHeu, sorry for the delay. You should be able to copy $FSLDIR/fslpython/envs/fslpython/bin/FSLeyes.app folder into your /Applications/ folder, e.g.:

cp -r $FSLDIR/fslpython/envs/fslpython/bin/FSLeyes.app /Applicatiions/

Moreover, when I open FSLeyes from the terminal (which is working fine) the icon is named "python" and not "FSLeyes"

There's nothing I can do about this at the moment, I'm afraid - it's to do with how macOS/GUI apps are distributed as conda packages.

JohannaHeu commented 2 years ago

Thank you so much .. I think I now found the issue. Always when I call fsleyes in my terminal it opens an fsleyes but from another directory than from the directory you just gave me.

I found the fsleyes application in the direction you wrote and was able to copy it into my applications. But now when I call fsleyes from the terminal it will open the other fsleyes from the directory: usr/local/fsl/fslpython/envs/fslpython/python so as much as I understand, it does not take the right direction.

Is there any way I can change this, so that I will call the right application from my terminal as well?

Thank you!

pauldmccarthy commented 2 years ago

Hi @JohannaHeu, unless you have installed FSLeyes independently of your FSL installation, they will both be calling the same version - the FSLeyes.app directory just contains a simple script which calls the version of FSLeyes that is installed in $FSLDIR.

If you have installed FSLeyes separately (e.g. by running pip install fsleyes or conda install -c conda-forge fsleyes), you will need to figure out which python environment you have installed it into, and remove it.