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. >
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The information in this e-mail is intended only for the person to whom
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