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 <chenchunhuich...@gmail.com> Date: Friday, November 1, 2013 2:55 AM To: Matt Glasser <m...@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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
