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 >> > >
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