Re^2: Loop is not working

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,

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Re^3: Loop is not working by Marshall (Canon) on Oct 04, 2018 at 01:14 UTC
In general, I would not do a chdir from the Perl script and prefer to use a path name. But if you do a chdir, you should check for success. Did `chdir "/mnt/hgfs/ExpAutism/Scripts";` work? -> check the result of all file system operations. In general, I've found that changing the running default directory causes more problems than it fixes. Just a thought.	[reply] [d/l]
Re^4: Loop is not working by haukex (Archbishop) on Oct 04, 2018 at 07:24 UTC
I completely agree that absolute pathnames and writing scripts to be independent of the current working directory is a good thing. In addition to error checking, I'd also recommend using a module to make operations on filenames platform independent (File::Spec, Path::Class, Path::Tiny, etc.). Unfortunately, external programs aren't always written like that, and may depend on the current working directory (just one example of many would be git). In those cases, I like to use File::pushd to make changes to the current working directory temporary.	[reply]
Re^3: Loop is not working by haukex (Archbishop) on Oct 04, 2018 at 07:15 UTC
`die "$program $outfile failed: $?";` ... `C/usr/local/fsl/bin/feat Level1Run1_test_spec.fsf failed: 2 at Level1Run1_test.pl` ... what does "2" mean there? See $? and system for the interpretation of values of `$?`. In this case, it means that the program exited due to signal nr. 2, which normally corresponds to `SIGINT`, which normally corresponds to hitting Ctrl-C on your keyboard, and which would also explain the `C` at the beginning of your output (on my system, it shows as `^C`). So it looks like you hit Ctrl-C while `/usr/local/fsl/bin/feat` was running. If so, why did you do that?	[reply] [d/l] [select]
Re^3: Loop is not working by NetWallah (Canon) on Oct 03, 2018 at 23:35 UTC
How did "C" get pre-pended in the output: `C/usr/local/fsl/bin/feat` [download] ? The assignment was : `my $program = '/usr/local/fsl/bin/feat';` [download] which should have worked. If you need the drive letter, use "C:". Memory fault -- brain fried	[reply] [d/l] [select]
Re^3: Loop is not working by stevieb (Canon) on Oct 03, 2018 at 23:16 UTC
This is a huge guess here, but I feel that this is due to a `#define ENOENT 2 /* No such file or directory */` that may have been encountered. You may be in a directory that you think you are but aren't, or possibly trying to work on a file from a location where it doesn't exist. Can you change: `system($program,$outfile) == 0 or die "$program $outfile failed: $?";` [download] ...to: `print -x $program . "\n"; open my $fh, '<', $outfile or die $!;` [download] ...within the exact same code and see if you get an error?	[reply] [d/l] [select]