my @dirs = ('/path/to/dir1', '/some/other/path/to/dir2', '/dir3');
for my $dir (@dirs) {
    ...
}
[download]

To populate the array with the names, you can use a map:

my @dirs = map { sprintf 'abc_%03d', $_ } 1 .. 100;
[download]

If you really need the array index, loop over the indices rather than the elements themselves:

for my $i (0 .. $#dirs) {
    my $dir = $dirs[$i];
    ...
}
[download]

In addition to choroba's (++) reply above, you might look at File::Find, a core module that does a lot of work for you. File::Find::Rule enables code that I find clearer, but it's not core.

Regards,

John Davies

Even with helpful indentation your sscript has errors. while : why the semicolon at the end? continue { } what do you want to do with that? answer to me: well to increment $i obviously.

$i=1;
while ($i<=4);
{
  chdir ($i) or die "Konnte Verzeichnis $i 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 ("..");
}

continue
{
$i ++;
}
[download]

In order to construct a filename from a basename and an index, as others said, just concatenate the basename with the index: my $filename = 'abc_' . sprintf("%.3d", $i); (note the 3-zero padding convention). Or File::Find the files you want (based on a regex pattern) as some other monk said.

For chdir back to your current dir, this is more convenient for me:

use Cwd qw(cwd);
my $oridir = cwd;
chdir("a/b/c/");
...
# back to original dir
chdir($oridir);
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Of course there's also File::pushd which only halfway meets the convenience and simplicity of *nix's pushd/popd

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("..");
}
[download]

Because this is Perl, There Is More Than One Way To Do It. Here is an array-less solution given your statement about how the folders are named:

for ( my $i = 1; $i <= 4; $i++ ) {
    my $dir_name = sprintf 'abc_%03d', $i;
    chdir $dir_name or die "Unable to change to $dir_name: $!";
    ...
    chdir '..';
}

But in real life I would probably use File::Find like everyone else.

A perlish equivalent:

for my $i ('001' .. '004') {
    my $dir_name = "abc_$i";
    chdir $dir_name or die "Unable to change to $dir_name: $!";
    ...
    chdir '..';
}
[download]

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🦛