We'll use Ubuntu for this example, but essentially you need an ntfs-3g package, which contains ntfsfix. Under Ubuntu, run the following to install it:
sudo apt-get install ntfs-3g
Then this (where /dev/sdd1 would be your ntfs disk):
Depending on what you are trying to fix, you may want to use options -b and -d.
-d − attempts to fix dirty states of the disk
-b − attempts to fix bad sectors on the drive (or mark them as such, so they are not written to)
So your full command will be something like this:
ntfsfix -d -b /dev/sdd1
Add "sudo" if not running as root.