sure, i do it quite often.

i don't know how your code bt i suppose that, to detect motion, you do something like
- remember the old frame
- for x=0 to width and y=0 to height check for differences
- if difference is found do something (like color the moved pixel and/or store/increment a variable...)

if you want to look for movement in a cropped area instead of the full screen, you simply need to make a for cycle for every cropped area:

for x=crop_horizontal_orgin to crop_width and y=crop_vertical_origin to crop_height

ecc...