External Email - Use Caution 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 <skharooton...@ucdavis.edu> > wrote: > > > 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 > _______________________________________________ > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
