 }
 
 void advanceCycleNum(){
-  mirrorTTL3source = 10; //default polarized line beta shutter sequence
+  mirrorTTL3source = pinTTL_IN3_pol; //default polarized line beta shutter sequence
   mirrorTTL2 = true;  //default clock bias field TTL mirrored
   if (mode == 1) {
     cycleNum += 1;

#define setPinTTL_OUT2_HIGH() PORTC |= 0b00000010;
#define setPinTTL_OUT2_LOW() PORTC &= 0b11111101;

#define pinTTL_OUT3 12 //Source of mirrored TTL is set by mirrorTTL3source.
#define setPinTTL_OUT3_HIGH() PORTB |= 0b00010000;
#define setPinTTL_OUT3_LOW() PORTB &= 0b11101111;

volatile int cycleNum = 666;
volatile boolean mirrorTTL1 = true; // This is usually for varying systematics
volatile boolean mirrorTTL2 = true; // Used for mirroring the Clock Bias field on/off
volatile int mirrorTTL3source = pinTTL_IN3_pol; // 10 - source for beta shutter for polarized sequence
                                                // 11 - source for beta shutter for unpolarized sequence

void setup(){
  Serial_Init();
