This is similar to 008 » Stop CHKDSK from running at boot time.
Use Regedt32 to navigate to:
Double-click BootExecute in the right-hand pane. In the Multi-String Editor, change:
autoconv \DosDevices\<Drive:> /FS:NTFS
autocheck autochk *
See tip 0320 for the space required to perform a convert.
NOTE: If you have an additional drive or partition, see tip 1377.