If you must use 5.1 (I would recommend upgrading), then try what Zeke suggested there.
You beat me to the email ;) hth d On Thu, Jun 2, 2016 at 3:41 PM, Joshua Lee <jki...@ucdavis.edu> wrote: > Perhaps something to do with > > libcrypt-2.*.so ?? > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040528.html > > - > Joshua Lee, Ph.D. > Post-Doctoral Researcher > MIND Institute > University of California, Davis > 530.747.3805 > > On Thu, Jun 2, 2016 at 12:36 PM, Joshua Lee <jki...@ucdavis.edu> wrote: >> >> I do note that I can enter "freeview ./brain.mgz" and the image opens. >> Then I can manuall save it as a .nii >> >> - >> Joshua Lee, Ph.D. >> Post-Doctoral Researcher >> MIND Institute >> University of California, Davis >> 530.747.3805 >> >> On Thu, Jun 2, 2016 at 12:33 PM, Joshua Lee <jki...@ucdavis.edu> wrote: >>> >>> I had replaced the user name in the output I posted to the listserv for >>> security reasons. I am not on a virtual machine. Fresh install on bare >>> metal. >>> ls -l ../ >>> >>>> ... >>>> drwxr-xr-x 13 myuser myuser 4096 Jun 2 11:50 mri >>>> ... >>>> >>> >>> - >>> Joshua Lee, Ph.D. >>> Post-Doctoral Researcher >>> MIND Institute >>> University of California, Davis >>> 530.747.3805 >>> >>> On Thu, Jun 2, 2016 at 12:25 PM, dgw <dgwake...@gmail.com> wrote: >>>> >>>> Is this a virtual machine? (The username seems odd...) >>>> >>>> What is the output of whoami? >>>> >>>> What is the output of ls -l ../? >>>> >>>> hth >>>> d >>>> >>>> >>>> >>>> On Thu, Jun 2, 2016 at 3:19 PM, Joshua Lee <jki...@ucdavis.edu> wrote: >>>> > Hi Doug, >>>> > >>>> > Yes the quoted lines were output fromt her terminal. >>>> > >>>> >> ls -l brain.mgz >>>> >> -rwxrwx--- 1 myuser myuser 1216430 May 18 17:06 brain.mgz >>>> > >>>> > >>>> > I have many Tb of disk space. I can chmod 777 the files and still seg >>>> > faults. >>>> > >>>> > Thanks >>>> > Josh >>>> > >>>> > >>>> > >>>> > - >>>> > Joshua Lee, Ph.D. >>>> > Post-Doctoral Researcher >>>> > MIND Institute >>>> > University of California, Davis >>>> > 530.747.3805 >>>> > >>>> > On Thu, Jun 2, 2016 at 12:13 PM, Douglas N Greve >>>> > <gr...@nmr.mgh.harvard.edu> >>>> > wrote: >>>> >> >>>> >> Can you send the full terminal output? Or is that it? Do you have >>>> >> enough >>>> >> disc space or is it running out? what is the result of >>>> >> ls -l brain.mgz >>>> >> >>>> >> >>>> >> >>>> >> On 06/02/2016 03:07 PM, Joshua Lee wrote: >>>> >> > On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on >>>> >> > Ubuntu 16.04 LTS >>>> >> > mri_convert is seg faulting >>>> >> > >>>> >> > >>>> >> > >>ls brain* >>>> >> > brain.finalsurfs.mgz brainmask.auto.mgz brainmask.mgz >>>> >> > brain.mgz >>>> >> > >>>> >> > mri_convert ./brain.mgz --in_type mgz --out_type nii -o >>>> >> > ./brain.nii >>>> >> > >>>> >> > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >>>> >> > reading from ./brain.mgz... >>>> >> > Segmentation fault (core dumped) >>>> >> > >>>> >> > >>>> >> > Any ideas? >>>> >> > >>>> >> > Thanks >>>> >> > >>>> >> > Joshua >>>> >> > >>>> >> > >>>> >> > >>>> >> > _______________________________________________ >>>> >> > Freesurfer mailing list >>>> >> > Freesurfer@nmr.mgh.harvard.edu >>>> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >> >>>> >> -- >>>> >> Douglas N. Greve, Ph.D. >>>> >> MGH-NMR Center >>>> >> gr...@nmr.mgh.harvard.edu >>>> >> Phone Number: 617-724-2358 >>>> >> Fax: 617-726-7422 >>>> >> >>>> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> >> Outgoing: >>>> >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >> >>>> >> _______________________________________________ >>>> >> Freesurfer mailing list >>>> >> Freesurfer@nmr.mgh.harvard.edu >>>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >> >>>> >> >>>> >> 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 >>>> >> http://www.partners.org/complianceline . 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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> > >>>> > >>>> > 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 >>>> > http://www.partners.org/complianceline . 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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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 > http://www.partners.org/complianceline . 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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
