External Email - Use Caution
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
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
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
External Email - Use Caution
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.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Glasser, Matthew 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
ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.
External Email - Use Caution
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
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
________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
External Email - Use Caution
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
External Email - Use Caution
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
ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.
External Email - Use Caution
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
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
________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
External Email - Use Caution
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
ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.
External Email - Use Caution
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
External Email - Use Caution
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
ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.
External Email - Use Caution
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
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
________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
freesurfer@nmr.mgh.harvard.edu
-
Glasser, Matthew -
Sanchez, Juan (NYSPI)