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Thanks for the reply Matt
freesurfer-i386-apple-darwin11.4.2-stable5-20130514
The scripts run fine outside of condor. So it must be how condor is selecting
the freesurfer
The Environment is set up correclty
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Glasser, Matthew
<glass...@wustl.edu>
Sent: Friday, October 26, 2018 4:26:13 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] cluster failing on HCP freesurfer script
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What version of FreeSurfer are you using? Is the FreeSurfer environment set up
correctly?
Matt.
From:
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Sanchez, Juan (NYSPI)"
<juan.sanc...@nyspi.columbia.edu<mailto:juan.sanc...@nyspi.columbia.edu>>
Reply-To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, October 26, 2018 at 3:12 PM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>"
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] cluster failing on HCP freesurfer script
External Email - Use Caution
Dear community,
My group is using the latest version of condor clustering to process our data
on OS X.
We have a bash script that calls freesurfer to run our HCP pipelines. I can run
the script to completion when running it locally on each of the clustered
machines, however when submitting the job I get the following error
Can’t locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup
module) (@INC contains:
/Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6
/Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18
/Network/Library/Perl/5.18/darwin-thread-multi-2level
/Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2
/System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18
/System/Library/Perl/Extras/5.18/darwin-thread-multi-2level
/System/Library/Perl/Extras/5.18 .) at
/Applications/freesurfer/mni/bin/nu_correct line 37.
BEGIN failed--compilation aborted at
/Applications/freesurfer/mni/bin/nu_correct line 37.
(standard_in) 2: comparison in expression
Can anyone suggest a solution?
Thanks
J
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