my $001= "prob_001";
my $002= "prob_002";
my $003= "prob_003";

@filter: ("001", "002", "003");

#Brainextraction
foreach ("001", "002", "003")

##</code><code>##

$ cat zombie
cp $1 $2

##</code><code>##

ken@titan ~/tmp/pm_11137850/whole_head
$ for i in `ls -1 wh_*`; do echo $i; cat $i; done
wh_001
W_001
wh_002
X_002
wh_003
Y_003
wh_004
Z_004

ken@titan ~/tmp/pm_11137850/just_brain
$ ls -l
total 0

##</code><code>##

#!/usr/bin/env perl

use strict;
use warnings;
BEGIN { delete @ENV{qw{PATH IFS CDPATH ENV BASH_ENV}} }
use autodie ':all';

use constant {
    INDIR  => '/home/ken/tmp/pm_11137850/whole_head',
    OUTDIR => '/home/ken/tmp/pm_11137850/just_brain',
    ZOMBIE => '/home/ken/tmp/pm_11137850/zombie',
};

use Getopt::Long;
my ($in_dir, $out_dir);
my $filter_string = '';
GetOptions(
    'indir=s'   => \$in_dir,
    'outdir=s'  => \$out_dir,
    'filters=s' => \$filter_string,
);
my @filters;
my @raw_filters = split /,/, $filter_string;
my @problems;
_set_dirs(\$in_dir, \$out_dir, \@problems);
_get_filters(\@raw_filters, \@filters, \@problems);
die @problems if @problems;

system(ZOMBIE, INDIR."/wh_$_", OUTDIR."/jb_$_") for @filters;

sub _get_filters {
    my ($raw_filters, $filters, $problems) = @_;
    my $re = qr{^(\d+)$};

    if (! @$raw_filters) {
        push @$problems, "No filters specified.\n";
    }
    else {
        for my $raw_filter (@$raw_filters) {
            if ($raw_filter =~ $re) {
                push @$filters, $1;
            }
            else {
                push @$problems, "Invalid filter: '$raw_filter'\n";
            }
        }
    }

    return;
}

sub _set_dirs {
    my ($in, $out, $problems) = @_;
    my $re = qr{^(\/[\w\/]+)$};

    if (length $$in) {
        if ($$in =~ $re) {
            $$in = $1;

            if (! -d $$in) {
                push @$problems, "Non-existent input directory: '$$in'\n";
            }
        }
        else {
            push @$problems, "Invalid input directory name: '$$in'\n";
        }
    }
    else {
        $$in = INDIR;
    }

    if (length $$out) {
        if ($$out =~ $re) {
            $$out = $1;

            if (! -d $$out) {
                push @$problems, "Non-existent output directory: '$$out'\n";
            }
        }
        else {
            push @$problems, "Invalid output directory name: '$$out'\n";
        }
    }
    else {
        $$out = OUTDIR;
    }

    return;
}

##</code><code>##

system(ZOMBIE, INDIR."/wh_$_", OUTDIR."/jb_$_") for @filters;

##</code><code>##

ken@titan ~/tmp/pm_11137850
$ perl -T ./pm_11137850_system.pl -filters 001,004

ken@titan ~/tmp/pm_11137850/just_brain
$ for i in `ls -1 jb_*`; do echo $i; cat $i; done
jb_001
W_001
jb_004
Z_004

##</code><code>##

ken@titan ~/tmp/pm_11137850
$ ./pm_11137850_system.pl -filters 003

ken@titan ~/tmp/pm_11137850/just_brain
$ for i in `ls -1 jb_*`; do echo $i; cat $i; done
jb_001
W_001
jb_003
Y_003
jb_004
Z_004

##</code><code>##

ken@titan ~/tmp/pm_11137850
$ ./pm_11137850_system.pl -outdir /fred -indir wilma
Invalid input directory name: 'wilma'
Non-existent output directory: '/fred'
No filters specified.