Just to amplify on what joost advised, you can "sometimes" get better results with a piped open command, if you pipe open a bash shell interpreter, then print commands to it. Like:

#!/usr/bin/perl
use warnings;
use strict;
use IPC::Open3;

$|=1;

#my $pid=open3(\*IN,\*OUT,\*ERR,'/bin/bash'); 
my $pid=open3(\*IN,\*OUT,0,'/bin/bash');
# set \*ERR to 0 to send STDERR to STDOUT 

my $cmd = 'matlab -interactive';
#send cmd to bash 
print IN "$cmd\n";

#getresult 
my $result = <OUT>;
print $result;
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The reason I mention it, is that matlab(which I don't use, so this is speculation) may act funny in interactive mode, unless it is running from a shell. So if

my $pid=open3(\*IN,\*OUT,0, '/usr/bin/matlab');
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dosn't seem to work well, try the above trick.

Another thing I will mention, is that if you are doing huge number calculations, you may run into a problem with the 4k buffer that IPC uses on linux. In case you are curious, see what I did for running the 'bc' calculator, and getting huge output at IPC3 buffer limit problem