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 DENSE ROI
   wb_command -backend-average-dense-roi
      <index-list> - comma separated list of cifti indexes to average
      <out-file> - file to write the average row to

      This command is probably not the one you are looking for, try
      -cifti-average-dense-roi.  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.