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HSDIO 6541 aquisition speed

I am trying to read data packets that are coming at a rate of 1KHz.  I have 4 data lines, a 32khz clock,  and a data start line at 1KHz.   I am read all 6 lines so I can process the data properly.  I am using an onboard clock at 1Mhz and reading 210 data points.  I am triggering on a data start line using PFI1 and reading 210us worth of data.  The HSDIO read is taking 2ms to execute so I am missing half of the data.  Is that any way to speed up the data read so that I don't miss any of the data start triggers.

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