reset permission

The System folder permissions are corrupted and Administrator doesn't have permission to reset them to default, i.e. icacls won't work and neither does anything else.
SFC and DISM don't return any errors but some services don't have access to files that they should have.
Is there a repair for this? I am not sure if Windows Reinstal/repair using an image works. I thought I saw an option for DELL to this rather than using a Microsoft Windows Image file.
IS there such an option.
I have to many apps and development tools to reformat the disk and install everything from scratch.
I am hoping that there is a better solution.