Ubuntu: Repair ntfs

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Install ntfs-3g with sudo apt-get install ntfs-3g. Then run the ntfsfix command on your NTFS partition.

For example:

ntfsfix /dev/hda6

   ntfsfix v2.0.0 (libntfs 10:0:0)

   Usage: ntfsfix [options] device

   Attempt to fix an NTFS partition.

   -h, --help             Display this help
   -V, --version          Display version information

   Developers' email address:

   linux-ntfs-dev@lists.sf.net Linux NTFS homepage: http://www.linux-ntfs.org

For newer Ubuntus You can use -b and -d option together. -b tries to fix bad clusters and -d to fix dirty states. So the command can be

sudo ntfsfix -b -d /dev/sda6

--help shows them

ntfsfix v2015.3.14AR.1 (libntfs-3g)

Usage: ntfsfix [options] device
    Attempt to fix an NTFS partition. 

    -b, --clear-bad-sectors Clear the bad sector list
    -d, --clear-dirty       Clear the volume dirty flag
    -h, --help              Display this help
    -n, --no-action         Do not write anything
    -V, --version           Display version information