Checkout ntfsclone
. Eu acredito que é o que você está procurando.
Na página man
:
ntfsclone will efficiently clone (copy, save, backup, restore) or rescue an NTFS filesystem to a sparse file, image, device (partition) or standard output. It works at disk sector level and copies only the used data. Unused disk space becomes zero (cloning to sparse file), encoded with control codes (saving in special image format), left unchanged (cloning to a disk/partition) or filled with zeros (cloning to standard output).