suppress start message of Matlab

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Try using the -logfile command line option:

-logfile log         - Make a copy of any output to the command window
                       in file log. This includes all crash reports.

Then you can easily remove the first few lines using any way you want (sed for example). Example:

matlab.exe -nosplash -nodesktop -nojvm -logfile out.log -r 'rand(3,3), exit'
sed '1,5d' out.log

Also if you are running from a script where you need it to finish running before continuing, use the -wait option:

-wait      - MATLAB is started by a separate starter program
           which normally launches MATLAB and then immediately
           quits. Using the -wait option tells the starter
           program not to quit until MATLAB has terminated.
           This option is useful when you need to process the
           the results from MATLAB in a script. The call to
           MATLAB with this option will block the script from
           continuing until the results are generated.

More info on MATLAB startup options can be found here, or in the matlab executable reference pages: Windows/Unix

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