External Email - Use Caution 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...@rcmd.org> wrote: > 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 <skharooton...@ucdavis.edu> > wrote: > > > > > > External Email - Use Caution > > > > 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 > > > > -- > > > > 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
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