Permission denied when using pop_saveset in command line but not from GUI

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Greetings,
I am trying to execute a script to edit some electrophysiology data files (.set).
However, when attempting to use pop_saveset (a function from the package EEGLAB) within my script, I get the error that the file cannot be saved due to permission being denied. But when using the pop_saveset GUI, it saves the file just fine to the same location.
Any suggestions as to why this is happening, and how I can give MATLAB permission to write in this specific folder?
Thank you.

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