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Freesurfer not working on NeuroDesk Trial (test server) #59

Closed Andjelaaaa closed 2 years ago

Andjelaaaa commented 2 years ago

Hi @stebo85 ,

I tried testing out the neurodesk to use the freesurfer tool via the link you supplied and there seems to be a license issue. Do I need to add another license file as indicated ? Here is the shown error message below ERROR: FreeSurfer license file /usr/local/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. A path to an alternative license file can also be specified with the FS_LICENSE environmental variable. image

stebo85 commented 2 years ago

Dear @Andjelaaaa,

Yes, what you see is expected and the reason is that the Freesurfer Team does not allow a license file to be distributed and you need to apply for your own license if you want to use Freesurfer in Neurodesk.

This is described in the help when you open Freesurfer in Neurodesk:

image

For testing proposes you can do exactly what it says there:

echo "Steffen.Bollmann@cai.uq.edu.au
> 21029
>  *Cqyn12sqTCxo
>  FSxgcvGkNR59Y" >> ~/.license

then 

export FS_LICENSE=~/.license

then you can run all Freesurfer tools as expected.

Of you course instead of using my freesurfer license you need to apply for your own.

Can you please let me know if this works for you? (make sure the license file doens't contain > in the beginning of the line!)

Andjelaaaa commented 2 years ago

Thank you for your response! By following these steps, it now indeed works!