You won't be to run mathscript in FPGA; that is not supported. What you will have to do is to transfer data back and forth from the host to the FPGA using front panel controls or DMA. So, you can acquire data in FPGA, transfer data to host, do the math calculation and then transfer the data back, if necessary. Have a look at the examples in the Example Finder to find example of how to communicate between target and host and do post back if you have any questions after that.
