[Neurodebian-users] fsl_sub bug in 5.0.1

[Matt Glasser]

Hi FSL and Neurodebian Lists,

I have found a bug in the Neurodebian version of fsl_sub (not sure if it is
Neurodebian specific or present upstream in the FSL source as well).

Inside of the -q case:

    -q)
      queue="-q $2"
      qconf -sql | grep ^$queue 2>&1 >/dev/null
      if [ $? -eq 1 ]; then
  echo "Invalid queue specified!"
  exit 127
      fi
      shift;;

the flag -q is specified in the $queue variable before the qconf -sql test,
which causes the grep pipe to fail.

This can be changed like this:

      qconf -sql | grep ^$2 2>&1 >/dev/null

Other points:

POSIXLY_CORRECT is set by fsl_sub, however it causes some scripts to have
errors (FreeSurfer recon-all is one example, fsl_prepare_fieldmap that is
distributed with FSL is another):
POSIXLY_CORRECT=1
export POSIXLY_CORRECT

This should probably be unset after the arguments are parsed with getopt:
unset POSIXLY_CORRECT

Finally, FSLPARALLEL appears not to be exported in the Neurodebian version
of /etc/fsl/5.0/fsl.sh.

Thanks,

Matt.


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