Maybe its because its not an older version of that file from Ubuntu 12.04. All the data is processed on a different machine, but I then import it on my local machine for running different kinds of analyses (e.g. qdec). Will it matter if I use the latest FreeSurfer version with data processed on 5.1?
Josh - Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805 On Thu, Jun 2, 2016 at 1:13 PM, Joshua Lee <jki...@ucdavis.edu> wrote: > Unfortunately this does not seem to work. > > locate libcrypt-2 > > > */lib/x86_64-linux-gnu/libcrypt-2.23.so > <http://libcrypt-2.23.so>/lib32/libcrypt-2.23.so <http://libcrypt-2.23.so>* > > cp /lib/x86_64-linux-gnu/libcrypt-2.23.so > $FREESURFER_HOME/lib/libcrypt.so.1 > > [verified it copied, and added to lib path to environment] > > echo $LD_LIBRARY_PATH > > > */home/myuser/Tools/freesurfer/lib:/usr/lib/fsl/5.0* > > cd ~/data/APP_FreeSurfer/APP_longitudinal/100604-200/mri > ls brain.* > > *brain.mgz* > > mri_convert -i ./brain.mgz -o ./help.nii > > > > *$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)* > > > - > Joshua Lee, Ph.D. > Post-Doctoral Researcher > MIND Institute > University of California, Davis > 530.747.3805 > > On Thu, Jun 2, 2016 at 12:44 PM, dgw <dgwake...@gmail.com> wrote: > >> 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 >> > >
_______________________________________________ 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.
