Yogesh: For Brdu protocol you need to inject your animals initially with Brdu and continue dosing until u sacrifice. If you already got the tissues the only thing I can suggest is use of PCNA or Ki67 along with NeuN antibody.
As said Christopher, you may specify what do you want really, analyzing your results of neurogenesis or to perform neurogenesis. If the second option, you want, some answers have been given above, notably concerning the use of BrdU and if you are interested I can give you more informations.
OK ! You have to use 3 animal groups : Control, Stroke group and Stroke-treated group. You have to administrate BrdU 50mg/Kg 2X/day (12h between the two IP injections) for 5 days) during the same period for the 3 groups.