G'day perlnewbie,

Welcome to the Monastery.

"I think there a lot of syntax errors"

Yes, there are but these seem to have been addressed. I was concerned with this block of code:

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

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

#Brainextraction
foreach ("001", "002", "003")
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I may be wrong, but it looks like you were planning to, or at least thinking about, using symbolic references. This is generally considered to be a bad move and I would recommend that you steer clear of them until you're more experienced; even then, think very carefully before using them.

Follow the link I provided. Note that they can easily result in coding errors or simply confusing code. Your lexical (my) variables do not work with this mechanism. Perhaps inadvertently, you've expressly forbidden your code from using them (with use strict;): it will abort compilation if you attempt to do it. The strict pragma restricts their usage for a very good reason.

"In my script I want the outputimage to be saved in an other folder. Could anyone help me with this?"

I would set up default paths for your input and output directories; then allow users to specify alternatives via options. I would include thorough checking of all input from options and clean any tainted data (see perlsec for more about that).

Unsurprisingly, I have neither the bet program nor any MRI data. For testing, I set up an extremely minimal script to replace bet:

$ cat zombie
cp $1 $2
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and two directories, whole_head and just_brain, for input and output, respectively. The former has four tiny files, the latter starts empty:

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
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Here's the code (pm_11137850_system.pl):

#!/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 $$out) {
                push @$problems, "Non-existent output directory: '$$ou
+t'\n";
            }
        }
        else {
            push @$problems, "Invalid output directory name: '$$out'\n
+";
        }
    }
    else {
        $$out = OUTDIR;
    }

    return;
}
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You'll obviously need to make a number of changes for your own needs: the paths with '/home/ken/...'; perhaps s/ZOMBIE/BETCMD/; the regexes for checking user input; and so on.

Do note that the system() function takes a list. You'll probably want to expand my simplistic one line

system(ZOMBIE, INDIR."/wh_$_", OUTDIR."/jb_$_") for @filters;
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to include some error checking, handling and reporting. And, obviously, the list of arguments will need to be changed.

Take a look at Getopt::Long to change or extend options. Also, the "Documentation and help texts" section, along with Pod::Usage, for an improved user experience.

Here's a sample run showing that there's no tainting:

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
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Here's another showing what would probably be more normal usage:

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
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Here's some example error messages:

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.
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