Hi Julesjay,
It sounds like you might also run into a couple of other issues.
First, the SCXI-1122 has a selectable lowpass filter cutoff frequency of 4 Hz or 4 kHz. You can't turn off the filter. When you acquire waveforms at 50 kS/s with the SCXI-1122, all frequencies above 4 kHz will be severely attenuated. Depending on the width of the pulse you are trying to measure, this might be exactly what you want, or it might be a showstopper.
Second, it sounds like you want to use an analog reference trigger on the first channel of your task so that you can acquire 100 pre-trigger samples. M Series and E Series multifunction DAQ boards only support analog reference trigger from a channel in the task when there is one channel in the task. If there were multiple channels in the task, the switching of the input multiplexer would cause the reference trigger to happen early. This doesn't happen for start triggered tasks that acquire post-trigger samples. 
To work around this, you could connect your trigger signal to the APFI0 pin on the M Series using an SCXI-1180 feedthrough panel or the connector on the side of the SCXI-1349. However, the signal being wired to APFI0 would not go through the SCXI-1122, and would have to be attenuated externally. Digital reference trigger sources also are not subject to this restriction.
If you already are planning to use multiple SCXI-1122s, you might have more success by putting them in separate chassis and connecting them to separate M Series multifunction DAQ boards, synchronized over a RTSI cable, so that you could acquire from them simultaneously, but that would complicate your application code and require doubling up on more hardware. A different SCXI module might work: for example, the SCXI-1104C has an input range of +/ 60 VDC and has a 10 kHz lowpass filter cutoff frequency, but you would still be limited to one channel for analog reference triggering, if that is indeed a requirement. An S Series simultaneously sampling board or an isolated counter-timer board like the PCI-6624 might also be more appropriate, depending on the specifics of the pulses you are trying to measure. If you haven't already done so, I would recommend having our sales representatives (
http://www.ni.com/contact) help you find the best product for your application. 
Brad
					
				
			
			
				
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Brad Keryan
NI R&D