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Hello Freesurfers,
I'm running recond-all and getting ERROR: nu_correct. I see a lot of people online have had this problem but I've failed to found a solution. Any suggestions?
I'm running freesurfer on a virtual machine and I've attached my recon-all.log
thanks, sev
External Email - Use Caution
Dear Sevan,
Which version of FreeSurfer are you running on which system (Mac, Linux?), and what is the exact command line and error message?
In case it is about nu_correct not being found: it should be in $FREESURFER_HOME/mni/bin/nu_correct, and if you get that error, most likely your environment variable $FREESURFER_HOME is not setup correctly for your shell.
Please also report the output of these 2 commands so we can know more:
1) echo $FREESURFER_HOME 2) ls -l $FREESURFER_HOME/mni/bin/nu_correct
Best,
Tim
On April 1, 2019 at 2:22 AM Sevan Harootonian skharootonian@ucdavis.edu wrote:
External Email - Use CautionHello Freesurfers,
I'm running recond-all and getting ERROR: nu_correct. I see a lot of people online have had this problem but I've failed to found a solution. Any suggestions?
I'm running freesurfer on a virtual machine and I've attached my recon-all.log
thanks, sev
--
Sevan Harootonian research specialist
Ekstrom's Lab University of Arizona Psychology Department _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
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Hi Tim,
I'm running freesurfer on linux. And the exact error is:
ncvarput: ncid 5: Protocol error miicv_put: MINC package entry point nu_estimate_np_and_em: crashed while running mincmath (termination status=768) nu_correct: crashed while running nu_estimate_np_and_em (termination status=768) ERROR: nu_correct Linux neurodebian 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt9-3~deb8u1 (2015-04-24) x86_64 GNU/Linux
here are the outputs for the directories. 1) /home/brain/freesurfer 2)-rwxr-xr-x 1 brain brain 20569 Jun 19 2015 /home/brain/freesurfer/mni/bin/nu_correct
Any idea? I've tried it on several datasets and still the problem, though the example data sample-001.nii.gz doesn't throw this error.
best, sev
On Mon, Apr 1, 2019 at 1:43 AM Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use CautionDear Sevan,
Which version of FreeSurfer are you running on which system (Mac, Linux?), and what is the exact command line and error message?
In case it is about nu_correct not being found: it should be in $FREESURFER_HOME/mni/bin/nu_correct, and if you get that error, most likely your environment variable $FREESURFER_HOME is not setup correctly for your shell.
Please also report the output of these 2 commands so we can know more:
- echo $FREESURFER_HOME
- ls -l $FREESURFER_HOME/mni/bin/nu_correct
Best,
Tim
On April 1, 2019 at 2:22 AM Sevan Harootonian skharootonian@ucdavis.edu
wrote:
External Email - Use CautionHello Freesurfers,
I'm running recond-all and getting ERROR: nu_correct. I see a lot of
people
online have had this problem but I've failed to found a solution. Any suggestions?
I'm running freesurfer on a virtual machine and I've attached my recon-all.log
thanks, sev
--
Sevan Harootonian research specialist
Ekstrom's Lab University of Arizona Psychology Department _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hm, that's not the error I thought you were getting. nu_correct is on your PATH and your setup looks good.
I've never seen such an error, sorry.
Best,
Tim
On April 4, 2019 at 9:40 AM Sevan Harootonian skharootonian@ucdavis.edu wrote:
External Email - Use CautionHi Tim,
I'm running freesurfer on linux. And the exact error is:
ncvarput: ncid 5: Protocol error miicv_put: MINC package entry point nu_estimate_np_and_em: crashed while running mincmath (termination status=768) nu_correct: crashed while running nu_estimate_np_and_em (termination status=768) ERROR: nu_correct Linux neurodebian 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt9-3~deb8u1 (2015-04-24) x86_64 GNU/Linux
here are the outputs for the directories.
- /home/brain/freesurfer
2)-rwxr-xr-x 1 brain brain 20569 Jun 19 2015 /home/brain/freesurfer/mni/bin/nu_correct
Any idea? I've tried it on several datasets and still the problem, though the example data sample-001.nii.gz doesn't throw this error.
best, sev
On Mon, Apr 1, 2019 at 1:43 AM Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use CautionDear Sevan,
Which version of FreeSurfer are you running on which system (Mac, Linux?), and what is the exact command line and error message?
In case it is about nu_correct not being found: it should be in $FREESURFER_HOME/mni/bin/nu_correct, and if you get that error, most likely your environment variable $FREESURFER_HOME is not setup correctly for your shell.
Please also report the output of these 2 commands so we can know more:
- echo $FREESURFER_HOME
- ls -l $FREESURFER_HOME/mni/bin/nu_correct
Best,
Tim
On April 1, 2019 at 2:22 AM Sevan Harootonian skharootonian@ucdavis.edu
wrote:
External Email - Use CautionHello Freesurfers,
I'm running recond-all and getting ERROR: nu_correct. I see a lot of
people
online have had this problem but I've failed to found a solution. Any suggestions?
I'm running freesurfer on a virtual machine and I've attached my recon-all.log
thanks, sev
--
Sevan Harootonian research specialist
Ekstrom's Lab University of Arizona Psychology Department _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Sevan Harootonian research specialist
Ekstrom's Lab University of Arizona Psychology Department _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Best,
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
freesurfer@nmr.mgh.harvard.edu
-
Sevan Harootonian -
Tim Schäfer