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I'm trying to change some permissions on a folder. I'm running FreeNAS and using the windows permissions settings (not Unix). If I right click the file and go to properties and then security, it shows that the only person who can make changes is the: root(Unix user\root).

NOTE: For obvious reasons I can't login to the windows share using the root user.

So how would I go about changing the settings to allow my account to change the permissions?

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For NTFS

In researching this I found this AskUbuntu Q&A titled: How do I use 'chmod' on an NTFS (or FAT32) partition?. According to this thread there are several ways to go about this.

Methods

  1. Control the permissions at mount time.

    $ sudo mount -t ntfs -o \
        rw,auto,user,fmask=0022,dmask=0000 /dev/whatever /mnt/whatever
    
  2. Using a user mapping file

    Contrary to what most people believe, NTFS is a POSIX-compatible¹ filesystem, and it is possible to use permissions on NTFS.

    Consult the ntfs-3g man page as well as this ntfs-3g documentation on advanced ownership and permissions. The user mappings is covered in this topic titled: User Mapping.

    You can then generate a usermap file like so:

    ss #1

    ss #2

For CIFS

In your case you're dealing with CIFS (shares mounted via mount.cifs) so the above would not be applicable. In that case you can use the command-line tools getcifsacl & setcifsacl. The man page for setcifsacl has the following examples:

Add an ACE
   $ setcifsacl -a "ACL:CIFSTESTDOM\user2:DENIED/0x1/D" <file_name>
   $ setcifsacl -a "ACL:CIFSTESTDOM\user1:ALLOWED/OI|CI|NI/D" <file_name>
Delete an ACE
   $ setcifsacl -D "ACL:S-1-1-0:0x1/OI/0x1201ff" <file_name>
Modify an ACE
   $ setcifsacl -M "ACL:CIFSTESTDOM\user1:ALLOWED/0x1f/CHANGE" <file_name>
Set an ACL
   $ setcifsacl -S "ACL:CIFSTESTDOM\Administrator:0x0/0x0/FULL,
   ACL:CIFSTESTDOM\user2:0x0/0x0/FULL," <file_name>

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