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Interrupts and RTX questions

Hello,
I have a simple question about interrupt using the RTX. I have read the thread www.keil.com/.../rlarm_ar_inter_funct.htm to understand how RTX works for interrupts. It is clearly not recommended to use the NVIC. However I want to use the Stop Mode woken up every 3sec by alarm. The thing is that the RM (Table10.Stop Mode) says, clearly as well, that the NVIC must be enabled to wake up from an interrupt. I'm sure I don't really understand how to handle interrupts in RTX because it's my firts RTOS development that is why I rather like to ask experts ;)
Another thing, I've noticed that in the stop mode example given with uvision, the systick is disable before entering stop mode et re-enable after. I tried to let it running as I thought that entering the stop mode would stop any clock automatically and found that it did not work anymore ? Should I always do the same ? Will it imply some consequences with the RTX as it works on the Systick...
I hope it is clear and that there are not lots of mistakes but I did my best to explain my questions.
Regards,
Gary