Update registerSlice to loop through each channel

Now passing number of channels (chs) and which channel s currently is (ch).  It performs the alignment on the current channel and slice as compared to the target slice and channel, then it loops the transformation part so that it performs the transformation on all of the channels.  Had to redefine s and Filesaver sourcefile as not final, because we have to change which slice we are on (s) and the saved image (sourcefile) for each channel.