Thanks to everyone for commenting on my question. I just added the following line  use diagnostics; and reran the code. The loop worked successfully, and the result seems to be okay too. However, I received this long and confusing message in the terminal. What does this message mean exactly?

sluser@localhost Scripts]$ perl Level1Run1_test.pl
1538605204768    addons.update-checker    WARN    onUpdateCheckComplet
+e failed to parse update manifest: [Exception... "Update manifest is 
+missing a required addons property."  nsresult: "0x80004005 (NS_ERROR
+_FAILURE)"  location: "JS frame :: resource://gre/modules/addons/Addo
+nUpdateChecker.jsm :: getRequiredProperty :: line 473"  data: no] Sta
+ck trace: getRequiredProperty()@resource://gre/modules/addons/AddonUp
+dateChecker.jsm:473 < parseJSONManifest()@resource://gre/modules/addo
+ns/AddonUpdateChecker.jsm:483 < UpdateParser.prototype.onLoad/parser(
+)@resource://gre/modules/addons/AddonUpdateChecker.jsm:655 < UpdatePa
+rser.prototype.onLoad()@resource://gre/modules/addons/AddonUpdateChec
+ker.jsm:675 < UpdateParser/<()@resource://gre/modules/addons/AddonUpd
+ateChecker.jsm:593
1538605204784    addons.update-checker    WARN    onUpdateCheckComplet
+e failed to parse update manifest: [Exception... "Update manifest is 
+missing a required addons property."  nsresult: "0x80004005 (NS_ERROR
+_FAILURE)"  location: "JS frame :: resource://gre/modules/addons/Addo
+nUpdateChecker.jsm :: getRequiredProperty :: line 473"  data: no] Sta
+ck trace: getRequiredProperty()@resource://gre/modules/addons/AddonUp
+dateChecker.jsm:473 < parseJSONManifest()@resource://gre/modules/addo
+ns/AddonUpdateChecker.jsm:483 < UpdateParser.prototype.onLoad/parser(
+)@resource://gre/modules/addons/AddonUpdateChecker.jsm:655 < UpdatePa
+rser.prototype.onLoad()@resource://gre/modules/addons/AddonUpdateChec
+ker.jsm:675 < UpdateParser/<()@resource://gre/modules/addons/AddonUpd
+ateChecker.jsm:593
1538605204810    addons.update-checker    WARN    onUpdateCheckComplet
+e failed to parse update manifest: [Exception... "Update manifest is 
+missing a required addons property."  nsresult: "0x80004005 (NS_ERROR
+_FAILURE)"  location: "JS frame :: resource://gre/modules/addons/Addo
+nUpdateChecker.jsm :: getRequiredProperty :: line 473" 
 data: no] Stack trace: getRequiredProperty()@resource://gre/modules/a
+ddons/AddonUpdateChecker.jsm:473 < parseJSONManifest()@resource://gre
+/modules/addons/AddonUpdateChecker.jsm:483 < UpdateParser.prototype.o
+nLoad/parser()@resource://gre/modules/addons/AddonUpdateChecker.jsm:6
+55 < UpdateParser.prototype.onLoad()@resource://gre/modules/addons/Ad
+donUpdateChecker.jsm:675 < UpdateParser/<()@resource://gre/modules/ad
+dons/AddonUpdateChecker.jsm:593
1538605204818    addons.update-checker    WARN    onUpdateCheckComplet
+e failed to parse update manifest: [Exception... "Update manifest is 
+missing a required addons property."  nsresult: "0x80004005 (NS_ERROR
+_FAILURE)"  location: "JS frame :: resource://gre/modules/addons/Addo
+nUpdateChecker.jsm :: getRequiredProperty :: line 473"  data: no] Sta
+ck trace: getRequiredProperty()@resource://gre/modules/addons/AddonUp
+dateChecker.jsm:473 < parseJSONManifest()@resource://gre/modules/addo
+ns/AddonUpdateChecker.jsm:483 < UpdateParser.prototype.onLoad/parser(
+)@resource://gre/modules/addons/AddonUpdateChecker.jsm:655 < UpdatePa
+rser.prototype.onLoad()@resource://gre/modules/addons/AddonUpdateChec
+ker.jsm:675 < UpdateParser/<()@resource://gre/modules/addons/AddonUpd
+ateChecker.jsm:593
1538605204826    addons.update-checker    WARN    onUpdateCheckComplet
+e failed to parse update manifest: [Exception... "Update manifest is 
+missing a required addons property."  nsresult: "0x80004005 (NS_ERROR
+_FAILURE)"  location: "JS frame :: resource://gre/modules/addons/Addo
+nUpdateChecker.jsm :: getRequiredProperty :: line 473"  data: no] Sta
+ck trace: getRequiredProperty()@resource://gre/modules/addons/AddonUp
+dateChecker.jsm:473 < parseJSONManifest()@resource://gre/modules/addo
+ns/AddonUpdateChecker.jsm:483 < UpdateParser.prototype.onLoad/parser(
+)@resource://gre/modules/addons/AddonUpdateChecker.jsm:655 < UpdatePa
+rser.prototype.onLoad()@resource://gre/modules/addons/AddonUpdateChec
+ker.jsm:675 < UpdateParser/<()@resource://gre/modules/addons/AddonUpd
+ateChecker.jsm:593  
+ DONE +++
[download]

Just in case you need to see the code I used again:

#!/usr/bin/perl
use strict;
use warnings;
use diagnostics;

# do second level statistical analysis run by run
# go to the directory where the fsf-file for stats 
# and post-stats is stored
chdir  "/mnt/hgfs/ExpAutism/Scripts";

my $infile  = 'Level1Run1_test.fsf';
my $outfile = 'Level1Run1_test_spec.fsf';
my $program = '/usr/local/fsl/bin/feat';

my @subjects = ("SubjectASD203","SubjectTD106C");
foreach my $subject (@subjects){
  open my $fh_IN, '<', $infile 
    or die "Could not open $infile ; $!";
  open my $fh_OUT, '>', $outfile 
    or die "Could not open $outfile ; $!";  
  # replace wildcards with specific titles of subjects
  while (<$fh_IN>){
    s/Subjectx/$subject/g;
    print $fh_OUT $_;            
  }
  close $fh_IN;
  close $fh_OUT;
  system($program,$outfile) == 0
        or die "$program $outfile failed: $?";
}        
print "\n +++ DONE +++ \n";
[download]

Thanks a ton!

Hi, that message seems to refer to an issue with your Mozilla-based browser. I don't know how this comes into play in your program; I did look at the source of feat a little bit and saw that it outputs HTML, so maybe related?

Anyway I wanted to point you to one of many ways to capture all the output from your external command, Capture::Tiny. You could use something like this to examine the output and perhaps see where the source of the message is:

use Capture::Tiny ':all';

my ($stdout, $stderr, $exit) = capture {
  system( $program, $outfile );
};

print sprintf('Stderr: >%s< Stdout: >%s<', $stderr, $stdout);

if ( $exit != 0 ) {
    die sprintf('%s exited with status %s.', $program, $exit;
}
[download]

Hope this helps!



The way forward always starts with a minimal test.

I agree with 1nickt that this looks like error messages from a Mozilla browser. At the moment I don't see the version of feat that 1nickt found launching a browser though - could you point us to where you got feat and its accompanying tools?

So in other words this isn't Perl outputting these messages, and I think you could probably just ignore them for now, as long as the rest of the code runs and the output looks good.

Hi everyone,

Thanks a lot for your help. Everything went smoothly and I could finish this analysis. I would not have had progressed this fast without your inputs. I really appreciated your help.

Thanks again and have a great weekend!

Best,