Calling linux functions from a Win 10 program


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Hi, I am looking for a way to call functions in a program running in Ubuntu (Afni, a data analysis tool) from Matlab.
I can call basic unix functions from Matlab directly (for example !ubuntu -c ls) but I can’t access this specific program (which lives in /home/myname/abin) or any of its functions which I would like to run from Matlab.
When I set the path to access the directory of this program in Matlab (using the matlab command setenv) the path is indeed set correctly. But whatever function I am trying to run, it is not recognized as a command.
I think this might be related with Windows being blind for Ubuntu directories or not having permission to access them but even setting the path directly to Ubuntu files stored in Windows (as decribed here: https://www.howtogeek.com/261383/how-to-access-your-ubuntu-bash-files-in-windows-and-your-windows-system-drive-in-bash/ ) does not do the job.
Before I reinstall Matlab in Ubuntu only to be able to access this program, does anyone know how to solve this problem?
 
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