Dear poj,

Thank you so much for your reply and precious time. I implemented your suggestion and here is the code: 

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

# do first 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]

The error message on the terminal:  C/usr/local/fsl/bin/feat Level1Run1_test_spec.fsf failed: 2 at Level1Run1_test.pl line 28. The line 28 is  system($program,$outfile) == 0

I am confused again. The problem seems to be with the feat file but what does "2" mean there? Do you have any suggestions?

PS1: The parent folder of each subject folder is /mnt/hgfs/ExpAutismand the parent folder of the fsf and pl files is  /mnt/hgfs/ExpAutism/Scripts

Thanks in advance. Best,

In reply to Re^2: Loop is not working by ozdemmer
in thread Loop is not working by ozdemmer

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