I do not think that one can define the initial guesses for center of clusters in matlab built-in function FCM. You can run the FCM a number of times and save the best result.
Thanks for all who answered the question. However, I believe the best way is to modify FCM module to accept input from another process. This way if I used an unsupervised technique which can provide initial cluster centers than the whole process becomes unsupervised
You could the code attached. A simple code of FCM for Matlab/Octave as a function. You could change the initial coordinates of cluster centers as you see fit.