Using Workbench Command

Workbench Command is a set of command-line tools that can be used to perform simple and complex operations within Connectome Workbench.

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CONNECTOME DB BACKEND COMMAND FOR CIFTI AVERAGE ROI CORRELATION
   wb_command -backend-average-roi-correlation
      <index-list> - comma separated list of cifti indexes to average and then
         correlate
      <out-file> - file to write the average row to

      This command is probably not the one you are looking for, try
      -cifti-average-roi-correlation.  It takes the list of cifti files to
      average from standard input, and writes its output as little endian,
      32-bit integer of row size followed by the row as 32-bit floats.