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 jkilee@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 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
> > 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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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.
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