I think the latest version of FSL has this sorted out (it doesn't change your machine's POSIXLY_CORRECT setting except briefly in the middle of fsl_sub).
Peace,
Matt.
From: chenchunhuichina chenchunhuichina@gmail.com Date: Friday, November 1, 2013 2:55 AM To: Matt Glasser matt@ma-tea.com Cc: free surfer freesurfer@nmr.mgh.harvard.edu Subject: ERROR: comparison in expression (FS with SGE)
Dear Matt and freesurfers,
I am encounting this old problem, that is, using fsl_sub to launch FreeSurfer jobs in SGE and get this error message: (standard_in) 2: Error: comparison in expression and freesurfer stoped. But running freesurfer without fsl_sub is OK (using fsl_sub to launch other commonds also fine).
Following Matt's message on this problem https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-May/023961.html, I added a line "POSIXLY_CORRECT=0 " in fsl_sub under the line "set -- `getopt T:q:a:p:M:j:t:z:N:Fvm:l:s: $*`" which now looks like this ... set -- `getopt T:q:a:p:M:j:t:z:N:Fvm:l:s: $*` POSIXLY_CORRECT=0 ...
However, the error was still the same, and what's even worse is that seems the job was launched twice.
So can Matt or anybody tell me why? Am I misunderstood Matt's message? or mybe version differences since Matt's solution came out one year ago? I am using freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0, FMRIB Software Library, Release 5.0 (c) 2012
there are two fsLsub ./src/sgeutils/fsl_sub ./bin/fsl_sub which one should I edit or both?
Any help is appreciated, Thank you all!
2013-11-01
Chunhui Chen _________________
State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875