Flip your images with e2proc2d.py before importing them, then treat them like cryo images (dark particles).
Here’s more detail for my approach: Easy template picking
Also you may need to change your CTF parameters. I would set the low resolution to something lower - so that the first peak isn’t masked, say 50 A. The amplitude contrast should be ~0.4. I recommend using CTFFIND4 over gCTF, and then always using the “fast” mode.
Good luck!