If the number of 'subject' folder names is small, your idea of putting them in an array has merit. Use foreach rather than while. 
se strict;
use warnings;

my @subjects = qw(abc_001 abc_002 abc_003);

foreach my $subject (@subjects) {
    chdir($subject) or die "Konnte Verzeichnis $subject nicht öffnen";

    foreach ( "T1_Map", "T2_Map", "PD_Map", "T2STAR_Map" ) {
        system("fslreorient2std $_.nii.gz $_._swapped.nii.gz");
        system("bet $_._swapped.nii.gz $_._swappedbrain.nii.gz -m");
    }

    chdir("..");
}

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Bill

In reply to Re: using an array in a while loop by BillKSmith
in thread using an array in a while loop by perlnewbie

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