Timer Interrupts on Due

Using this code, you can set a timer for any of the ISRs TC0_Handler through TC8_Handler, see table of parameters below. It is possible to use the timers without a physically mapped pin, such as TC1 channel 0 (TC3_Handler) shown here:

volatile boolean l;

//TC1 ch 0
void TC3_Handler()
{
        TC_GetStatus(TC1, 0);
        digitalWrite(13, l = !l);
}

void startTimer(Tc *tc, uint32_t channel, IRQn_Type irq, uint32_t frequency) {
        pmc_set_writeprotect(false);
        pmc_enable_periph_clk((uint32_t)irq);
        TC_Configure(tc, channel, TC_CMR_WAVE | TC_CMR_WAVSEL_UP_RC | TC_CMR_TCCLKS_TIMER_CLOCK4);
        uint32_t rc = VARIANT_MCK/128/frequency; //128 because we selected TIMER_CLOCK4 above
        TC_SetRA(tc, channel, rc/2); //50% high, 50% low
        TC_SetRC(tc, channel, rc);
        TC_Start(tc, channel);
        tc->TC_CHANNEL[channel].TC_IER=TC_IER_CPCS;
        tc->TC_CHANNEL[channel].TC_IDR=~TC_IER_CPCS;
        NVIC_EnableIRQ(irq);
}

void setup(){
        pinMode(13,OUTPUT);
        startTimer(TC1, 0, TC3_IRQn, 4); //TC1 channel 0, the IRQ for that channel and the desired frequency
}

void loop(){
}

Here is the table of parameters: