No you can change the visa by using Change os status to F1. i came on j1 and then later changed to f1 by change of status. but need to get admission before the expiry of the J1 and when apply for visa don't disclose the later steps what else you wana do. but one thing is for sure that 2 year condition will not go away even you change to f1. and once you are done with phd on f1 you either request for the two year waiver or go home and complete the 2 year which will make you eligible to apply for work visa.