The easiest way is to use MATLAB's Instrumentation Toolbox to implement serial communication with the FPGA. You will have to create a UART inside the FPGA to send data to and receive data from the PC. If you have a modern Altera or Xilinx FPGA development board, a serial-USB interface is provided for you.
On the PC side, with the Instrumentation Toolbox, MATLAB will provide functions to open, close and configure the serial port as well as functions for sending and receiving the data. You can write a MATLAB script with these functions to control communication with the FPGA.
On the FPGA side, the UART you created can receive the data from the serial port and send it to the other hardware functions you designed to process the data however you see fit.
I've done this a few times and it works well.
r.b.