If it did not autorun, try to tell it to do chkdsk again
Hit start and search for "cmd"
Right click it and select "Run as administrator"
This will give you an old fashioned command prompt window.
In that window you can just type it as you see "chkdsk c: /f"
If you have more then one drive or partition, you will need to tell it the disk(chkdsk d: /f).
If it is the primary windows disk(c:) it will ask you to schedule it for next boot. When you restart, it will do a chkdsk for you before even getting to the login screen.
If all goes well, you will be able to defrag, but be warned, the latest windows defrag is VERY slow. Something like Defraggler will work much faster and do as good of a job.
Its FREE http://www.piriform.com/defraggler