Hooper has shaken off the ankle complaint which ruled him out of the last two matches, only to fall ill on Thursday.
The top scorer was sent home by the doctor but will return to training on New Year's Day to see if he is well enough to feature at Glanford Park.
Midfielder Michael O'Connor has also been to the doctor and could miss the clash with diarrhoea-type symptoms.
Meanwhile, goalkeeper Josh Lillis could again replace Joe Murphy between the sticks as the regular shot-stopper struggles with a shoulder injury.
Josh Wright is also a doubt heading into the tie, having picked up a calf injury in the 3-1 defeat to West Brom on Monday. On the suspension front, Andrew Wright and Grant McCann miss the game following their red cards against the Baggies while Cliff Byrne returns from a ban.