The documentation for both of strcmp and strcmpi clearly states that they accept cell arrays of strings as the inputs:
>> A = {'my_string'};
>> B = {'my_string'};
>> strcmp(A,B)
ans =
1
It may be that your indexing is not working properly. Can you please give more details about the variables s1 and s2: their class, size and contents would be useful. Or perhaps you have nested cell arrays? In order to help you any further, we need to know about those variables!
This might be worth reading too:
