If you are using & after command I assume this command will not be finished ( until you dont forcefully do that ) , so you want matlab code to be executed after some desired operations (after which you want to execute your matlab code) of that command got finished.
One way is to redirect the output of command to some file and then parse the output and compare with some string which indicates the completion of the operation
Another way is to use expect script ( reference - https://stackoverflow.com/questions/17916201/background-spawned-process-in-expect)
