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 jkilee@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 dgwakeman@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 jkilee@ucdavis.edu wrote:
Perhaps something to do with
libcrypt-2.*.so ??
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040528...
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 jkilee@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 jkilee@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 dgwakeman@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 jkilee@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 > greve@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 >> greve@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
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