Installing the latest version of FreeSurfer has resolved this problem. So as long as the post-processing tools are compatible with these data then I should be fine.
Thanks. Josh - Joshua Lee, Ph.D. Post-Doctoral Researcher MIND Institute University of California, Davis 530.747.3805 On Thu, Jun 2, 2016 at 1:20 PM, Joshua Lee <jki...@ucdavis.edu> wrote: > 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 >>> >> >> >
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