I have no problem with Doom or Hexens but for some reason this game strains my eyes and gives me a headache after a few minutes. If I play the game for too long, it feels like I'm getting a fever.

Try playing it with eDuke instead. It's a different engine and you can use the high resolution pack. Maybe having 3D models instead of 2D sprites will help you?

You could also apply various graphical filters if it's too pixellated for you.

Thanks, it's a lot better with eDuke. It still strains my eyes more than other games but it doesn't cause headaches anymore.