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I have a 750D with just the stock fans and I plan on upgrading them to better fans in the future but I think if I'm going to invest in some better fans I should at least have better control over them. My motherboard only has 3 fan headers for case fans and the control on the headers is limited. I can't completely stop the fans and I can't change the temperature location on any of the headers they are all stuck on CPU temp. I was wondering if anyone knows of a good programmable fan controller that is maybe a PCI-e card or something...

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The NZXT Sentry 2 or 3 would be good choices. 

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If you are using motherboard headers, you will unfortunately be limited by them. 

 

Usually, the CPU fan headers will allow you to get the full spectrum of your fans, while the "SYS" headers will act a bit weird, not being able to lower your fans down to the lowest possible. 

 

If you want more control over what fan reacts to what, you should definitely give SpeedFan a try. It's a B to figure out and set up, but once you do it works wonders. It won't be able to get past the motherboard header limitations, though.

 

If you want absolute control on your fan rpm, you should get a hardware controller that connects directly to your PSU. It can either be DC based or PWM. I'm pretty sure there are some that can connect to a PWM header on your motherboard just to get a reading, but deal with the fans on their own. That coupled with SpeedFan might be what you're looking for.

 
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