convert C: /fs:ntfs at a command prompt, assuming it is the C: drive you want to convert. I can't find anything saying the system volume can't be converted, but you probably need a pure DOS (or similar)environment for this. Maybe start PC and press F8 during startup and choose to start with Command Prompt.
Note: Using this method the drive cannot be unconverted later. You must reformat the drive / partition if you want FAT32 back again.
You could also use Powerquest's Partition Magic (current version is 8). This will let you convert to NTFS and back again at a later date if absolutely necessary.