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):
ntfsfix /dev/sdd1
Depending on what you are trying to fix, you may want to use options -b and -d.