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.
