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my $dir = "usr/bin/Test_Protokoll"

my $dir = "usr/bin/Test_Protokoll";

#!/usr/bin/perl

...
    print "filter: $filter\n";    
    system("bet SYNT_MPRAGE_T1_PD_B0corr YNT_MPRAGE_T1_PD_B0corr_brain
+ -m");
}