Yeah, you'd need to unmount the drive with /x first, but since you're logged in that's not going to happen. I'd use a third party tool from a bootable disc for best results. There's a Linux disc that's supposed to be designed specifically for disk troubleshooting. I don't remember the name but it's easy enough to find on Distrowatch. Chkdsk isn't really very flexible, and many oldtimers have a distaste for it as it used to have a bad reputation.
Appears we have a
guide here on the site for Chkdsk, by the way.
[edit]I think the distro I mentioned was
Parted Magic.