NAS devices typically include their own operating system and configuration options. Many of the newer devices,
such as a Buffalo Terastation, let you join the device to Active Directory and set permissions to shares and files based on AD user accounts or group membership.
Without knowing the details of the NAS device that you are using, you will want to make sure to set permissions properly at the root of your data shares, and also configure them to propagate permissions to sub-folders and Windows NAS files.
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