This is what I did. I created a bootable .iso of the OS. In my case, I'm running windows 10 build 10041, so there are a few extra steps to create a bootable .iso version of this build. If you are also, you can google how to create the .iso, as the instructions are detailed and extensive. I then booted to a usb flash drive, with the .iso installed on it. The 2nd screen allows the choice of, "repair the computer". Next, I chose "Troubleshoot/Advanced Options/Run command prompt". From prompt, I ran "chkdsk C:". Checkdisk takes about an hour or so to complete. I rebooted when it finished and it booted up normally. If checkdisk does not work for you, there are still a number of other maintenance options available to you. One of them should work. I hope this helps.
edit: there are a number of other, less time consuming, possible solutions available on the OS install/repair media that should be attempted before my Checkdisk instructions. I'm just relaying what finally worked for me after exhausting all other possible repair solutions. Your results may vary.