Excluding a rectangular region from an image in FITS
Usually pixel coordinates.
What I would do is to let DS9 make a region file, as your documentation site says it supports them.

To do so:


Open file in ds9
From region->shape select the kind of region you want.
Click on edit->region
Draw the shapes you want (just click on the img)
Click region->save. In the coordinates box choose physical pixel coordinates.


Probably that should work... Good luck!