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 ++;
}
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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