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Thanks Matt
The Environment script actually sets up:
freesurfer-Darwin-lion-stable-pub-v5.3.0-HCP
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Glasser, Matthew glasserm@wustl.edu Sent: Friday, October 26, 2018 5:39:30 PM To: Freesurfer support list Subject: Re: [Freesurfer] cluster failing on HCP freesurfer script
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That seems like an old version to me.
Matt.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Sanchez, Juan (NYSPI)" <Juan.Sanchez@nyspi.columbia.edumailto:Juan.Sanchez@nyspi.columbia.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, October 26, 2018 at 3:43 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] cluster failing on HCP freesurfer script
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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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Glasser, Matthew <glasserm@wustl.edumailto:glasserm@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Sanchez, Juan (NYSPI)" <Juan.Sanchez@nyspi.columbia.edumailto:Juan.Sanchez@nyspi.columbia.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, October 26, 2018 at 3:12 PM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] cluster failing on HCP freesurfer script
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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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