Hi All, I am using the newest version of freesurfer, and I keep getting errors when I run recon-all -autorecon1. It appears that the error might have to do with nu_correct, and I have attached the recon-all.log. Any suggestions on how to fix this? Thanks,
Colleen Buckless Research Assistant Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute 443-923-2747 Buckless@kennedykrieger.org
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Hi Colleen, If you source freesurfer, and run: ls $FREESURFER_HOME/mni/bin It should output a list of mni tools, including nu_correct. Is this what you see? There's a possibility that your mni sub-directory isn't sourced. Andrew ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Buckless, Colleen Buckless@kennedykrieger.org Sent: Wednesday, July 05, 2017 12:18 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: [Freesurfer] error message while using autorecon1
Hi All, I am using the newest version of freesurfer, and I keep getting errors when I run recon-all –autorecon1. It appears that the error might have to do with nu_correct, and I have attached the recon-all.log. Any suggestions on how to fix this? Thanks,
Colleen Buckless Research Assistant Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute 443-923-2747 Buckless@kennedykrieger.org
________________________________ Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Hi Andrew, The output list includes nu_correct. Thanks, Colleen
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Hoopes, Andrew Sent: Wednesday, July 05, 2017 1:29 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] error message while using autorecon1
Hi Colleen, If you source freesurfer, and run: ls $FREESURFER_HOME/mni/bin It should output a list of mni tools, including nu_correct. Is this what you see? There's a possibility that your mni sub-directory isn't sourced. Andrew ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Buckless, Colleen Buckless@kennedykrieger.org Sent: Wednesday, July 05, 2017 12:18 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: [Freesurfer] error message while using autorecon1
Hi All, I am using the newest version of freesurfer, and I keep getting errors when I run recon-all -autorecon1. It appears that the error might have to do with nu_correct, and I have attached the recon-all.log. Any suggestions on how to fix this? Thanks,
Colleen Buckless Research Assistant Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute 443-923-2747 Buckless@kennedykrieger.org
________________________________ Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
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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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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.
After sourcing freesurfer, what comes up if you run the command "which nu_correct"? If it cannot find nu_correct on your path, do you mind telling me the method you use to source FS? Thanks, Andrew ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Buckless, Colleen Buckless@kennedykrieger.org Sent: Wednesday, July 05, 2017 1:36 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] error message while using autorecon1
Hi Andrew, The output list includes nu_correct. Thanks, Colleen
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Hoopes, Andrew Sent: Wednesday, July 05, 2017 1:29 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] error message while using autorecon1
Hi Colleen, If you source freesurfer, and run: ls $FREESURFER_HOME/mni/bin It should output a list of mni tools, including nu_correct. Is this what you see? There's a possibility that your mni sub-directory isn't sourced. Andrew ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Buckless, Colleen Buckless@kennedykrieger.org Sent: Wednesday, July 05, 2017 12:18 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: [Freesurfer] error message while using autorecon1
Hi All, I am using the newest version of freesurfer, and I keep getting errors when I run recon-all -autorecon1. It appears that the error might have to do with nu_correct, and I have attached the recon-all.log. Any suggestions on how to fix this? Thanks,
Colleen Buckless Research Assistant Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute 443-923-2747 Buckless@kennedykrieger.org
________________________________ Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
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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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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.
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I ran "which nu_correct" and it says command not found. What do you mean by the methods used to sourced FS? I am using a linux computing cluster to run FS on. Is this what you mean? Thanks, Colleen
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Hoopes, Andrew Sent: Wednesday, July 05, 2017 2:05 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] error message while using autorecon1
After sourcing freesurfer, what comes up if you run the command "which nu_correct"? If it cannot find nu_correct on your path, do you mind telling me the method you use to source FS? Thanks, Andrew ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Buckless, Colleen Buckless@kennedykrieger.org Sent: Wednesday, July 05, 2017 1:36 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] error message while using autorecon1
Hi Andrew, The output list includes nu_correct. Thanks, Colleen
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Hoopes, Andrew Sent: Wednesday, July 05, 2017 1:29 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] error message while using autorecon1
Hi Colleen, If you source freesurfer, and run: ls $FREESURFER_HOME/mni/bin It should output a list of mni tools, including nu_correct. Is this what you see? There's a possibility that your mni sub-directory isn't sourced. Andrew ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Buckless, Colleen Buckless@kennedykrieger.org Sent: Wednesday, July 05, 2017 12:18 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: [Freesurfer] error message while using autorecon1
Hi All, I am using the newest version of freesurfer, and I keep getting errors when I run recon-all -autorecon1. It appears that the error might have to do with nu_correct, and I have attached the recon-all.log. Any suggestions on how to fix this? Thanks,
Colleen Buckless Research Assistant Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute 443-923-2747 Buckless@kennedykrieger.org
________________________________ Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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.
Sourcing FS is something you need to do before running any freesurfer programs in a new shell (terminal). The steps to do this are described here: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Setup.26Configu...
The standard method (when using csh) involves running: setenv FREESURFER_HOME /usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh
which will set some environment variables and make all FS commands available to you. Sourcing FS like this should fix your issue with nu_correct, if not, this could be a bug.
best, Andrew ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Buckless, Colleen Buckless@kennedykrieger.org Sent: Wednesday, July 05, 2017 2:30 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] error message while using autorecon1
I ran "which nu_correct" and it says command not found. What do you mean by the methods used to sourced FS? I am using a linux computing cluster to run FS on. Is this what you mean? Thanks, Colleen
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Hoopes, Andrew Sent: Wednesday, July 05, 2017 2:05 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] error message while using autorecon1
After sourcing freesurfer, what comes up if you run the command "which nu_correct"? If it cannot find nu_correct on your path, do you mind telling me the method you use to source FS? Thanks, Andrew ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Buckless, Colleen Buckless@kennedykrieger.org Sent: Wednesday, July 05, 2017 1:36 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] error message while using autorecon1
Hi Andrew, The output list includes nu_correct. Thanks, Colleen
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Hoopes, Andrew Sent: Wednesday, July 05, 2017 1:29 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] error message while using autorecon1
Hi Colleen, If you source freesurfer, and run: ls $FREESURFER_HOME/mni/bin It should output a list of mni tools, including nu_correct. Is this what you see? There's a possibility that your mni sub-directory isn't sourced. Andrew ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Buckless, Colleen Buckless@kennedykrieger.org Sent: Wednesday, July 05, 2017 12:18 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: [Freesurfer] error message while using autorecon1
Hi All, I am using the newest version of freesurfer, and I keep getting errors when I run recon-all -autorecon1. It appears that the error might have to do with nu_correct, and I have attached the recon-all.log. Any suggestions on how to fix this? Thanks,
Colleen Buckless Research Assistant Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute 443-923-2747 Buckless@kennedykrieger.org
________________________________ Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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.
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freesurfer@nmr.mgh.harvard.edu
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Buckless, Colleen -
Hoopes, Andrew