You may run SFC offline:
SFC /SCANNOW : Run in Command Prompt at Boot
You can also do a disk check offline. Use
Advanced Boot Options to select Repair Your Computer and get to the
System Recovery Options. Then select the command prompt. Do the following:
chkdsk /r c:
chkdsk /r d:
chkdsk /r e:
chkdsk /r f:
.etc until you get the message that the volume could not be opened for direct access. For any drives that do not give the message:
"Windows has checked the file system and found no problems"
run chkdsk again as above. In other words, if it says:
"Windows has made corrections to the file system"
after running the disk check, run the disk check again.
I realize you may only have one disk show up in Windows explorer, but you may have more than one disk through recovery options. This is because the system creates a hidden boot partition (which will be C: in recovery), you may have a recovery partition for your PC that is hidden (which will be D: in recovery), and you will have your primary Windows partition (which may be E: in recovery). A custom PC will likely have at least C: and D: to scan.