A file system check in Linux is equivalent to chkdsk in Windows. It can only run on unmounted drive so if you want to run it on the next reboot, you can use the following command.

shutdown -rF now

Alternatively, you can also use the command below to schedule the fsck.

sudo touch /forcefsck

Done =)

Reference: nixCraft – Linux Force fsck on the Next Reboot or Boot Sequence