Which course should I choose if I get a chance to study at ISI Kolkata, a B.Math or a B.Stat?

Both B.Stat and B.Math are different courses being offered at different campuses at ISI Kolkata and ISI Bangalore respectively. There are only a few common subjects in both courses. 

The choice ultimately depends on your choice and interest. You can go through the syllabus of both courses and understand the topics. Find whichever interests you, you can choose to be research-oriented like B.math students or go for M.stat or other courses, if you choose so.

You can apply for only 1 course because the institute conducts the entrance of both courses at the same time and day. You will be able to appear for only one of them.