FFT butterfly input index
Assume $N=16$. so the counter $c$ chooses values between $0$ to $15$ and there are $s=1,2,\cdots,\log2(N)$ number of stages.
Based on your comment, the input-output relationship for stage $s$ can be given by:


Represent the counter in binary form in $\log_2 N$ bits (here 4 bits).
Circularly shift the counter $s-1$ times to the right.
Bit reverse the result.
Represent in decimal.


The following Matlab code can give the output in vector form as explained in the comment:

N = 16;
stage = 1              %Do it here for stage #1 
c = 0:N-1;
c_bin = de2bi(c);
butterfly_idx = bi2de(fliplr(circshift(c_bin',stage-1)'))


Example for N=16 and stage=2`:

c_bin =

     0     0     0     0
     1     0     0     0
     0     1     0     0
     1     1     0     0
     0     0     1     0
     1     0     1     0
     0     1     1     0
     1     1     1     0
     0     0     0     1
     1     0     0     1
     0     1     0     1
     1     1     0     1
     0     0     1     1
     1     0     1     1
     0     1     1     1
     1     1     1     1


fliplr(circshift(c_bin',1)')

ans =

     0     0     0     0
     0     0     1     0
     0     1     0     0
     0     1     1     0
     1     0     0     0
     1     0     1     0
     1     1     0     0
     1     1     1     0
     0     0     0     1
     0     0     1     1
     0     1     0     1
     0     1     1     1
     1     0     0     1
     1     0     1     1
     1     1     0     1
     1     1     1     1


bi2de(fliplr(circshift(c_bin',1)'))

ans =

     0
     4
     2
     6
     1
     5
     3
     7
     8
    12
    10
    14
     9
    13
    11
    15


which is the expected result for the second stage.