monline

Since this is invoked by one of the startup scripts of your OS, the exact behaviour might be a bit different depending on the implementation of your OS (and the specific OS version, eg. Ubuntu had this feature in /etc/init.d/checkfs.sh for quite a long time, then moved it somewhere else). The point is that at some step of your boot process the fsck tool is started with a set of commandline parameters. Eg. Ubuntu Hardy executes something like this:

Of course for this to work properly, only the root filesystem should be mounted. To get this right, you should boot the system either into single user mode or boot from a LiveCD (or LiveUSB) and chroot into your existing installation before executing the above command.

For a single filesystem you can execute something like this:

Or for ext4:

Of course the last argument should point to the device of your filesystem (which might be anything from /dev/sda1 to /dev/mapper/vol01-yourfilesystem or /dev/dm-3).

P.S.: AFAIK there's no "basic" and "thorough" fsck. If you run fsck with the -f (force) option, it'll do the same checks regardless of all the other options. So in the above examples the -a and -C0 (etc.) options do not change the "thoroughness" of fsck. A simple fsck.ext3 -f /dev/vol01/yourfilesystem will do just as well, but it'll ask you whether to fix any problems found and it'll not show you a progress bar so you'll never know whether it'll take another 3 hours or just 5 minutes to finish.