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The comparision can be mainly made on the basis of the bschool/university you are asking about because it is not necessary that the bschool you take admission in is good than the university or vice versa. The brand and its past review and existence guides you of what is better to choose.
IIMs are reputed bschools and on the other side FMS is choosen by students after IIM's. The percentile requirement is almost the same for both the institutes. The other facor is universities majorly provide MBA course which is of a fixed curriculum and bschools update their curriculum as per the needs and requirements. The fees structure does vary as the fees is high in bschools as compared to the latter. If you get any bschool/university you have to first aim high to get the one you wish to.
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