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?

In reply to Re^3: Loop is not working by haukex
in thread Loop is not working by ozdemmer

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