TIMER1 STM32F411 Resync

Hello, 

I have a signal that is coming to a GPIO and the period of the signal might slightly change and I need to realign a timer each time the GPIO is on rising edge.

I try to use the TIMER1 with Slave mode reset and use ETR1 as trigger source. but it is not really working the way I want 

I tried as well to catch the UIF interrupt and TIM1->CNT=0 but it is creating lagging.

How to do "Reset" the timer each time I receive a GPIO pulse ? thanks

Vincent