the following is a simple example showing you that you have full freedom:
>> a=magic(5)
a =
17 24 1 8 15
23 5 7 14 16
4 6 13 20 22
10 12 19 21 3
11 18 25 2 9
>> b=a(1:3,1:3)
b =
17 24 1
23 5 7
4 6 13
>> b=a(1:3,[1 3 5])
b =
17 1 15
23 7 16
4 13 22
>> b=a([1 2 4],[1 3 5])
b =
17 1 15
23 7 16
10 19 3
you can even try:
>> c=randint(3,3,sum(size(a)))+1
c =
10 9 7
5 6 9
5 3 1
>> b=a(c)
b =
18 12 5
11 24 12
11 4 17
where you know matlab count element in matrix column by column, for example, in this 2D 5x5 matrix, a(10)=a(5,2)