Hello,
I've used FreeSurfer previously on a linux machine (from a previous lab). Now, I have just installed it on a Mac OSX, using the "freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg" version. I followed all the instructions on the installation page. However, there were segfault errors when running both tkmedit and tksurfer as follows:
dyn-152-3-184-222:freesurfer joonkoopark$ more .xdebug_tkmedit
tkmedit started: Wed Jun 11 23:28:05 2014
/Applications/freesurfer/tktools/tkmedit.bin bert orig.mgz$Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /Applications/freesurfer Set subject home dir to /Applications/freesurfer/subjects/bert Using interface file /Applications/freesurfer/tktools/tkmedit.tcl
Segfault Setting global interpreter xDebug stack (length: 2) 01: main() 01: Setting global interpreter 00: 00: dyn-152-3-184-222:freesurfer joonkoopark$ more .xdebug_tksurfer
Segfault Initializing glut xDebug stack (length: 1) 00: 00: Initializing glut
Segfault Initializing glut dyn-152-3-184-222:freesurfer joonkoopark$
Any idea what went wrong and how to fix it?
Thank you!
Joon
Hi Joon,
What version of OSX are you on and have you installed XQuartz (http://xquartz.macosforge.org/landing/)? XQuartz is required for proper tkmedit/tksurfer functionality.
-Zeke
On 06/11/2014 11:48 PM, Joonkoo Park, Ph.D. wrote:
Hello,
I've used FreeSurfer previously on a linux machine (from a previous lab). Now, I have just installed it on a Mac OSX, using the "freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg" version. I followed all the instructions on the installation page. However, there were segfault errors when running both tkmedit and tksurfer as follows:
dyn-152-3-184-222:freesurfer joonkoopark$ more .xdebug_tkmedit tkmedit started: Wed Jun 11 23:28:05 2014 /Applications/freesurfer/tktools/tkmedit.bin bert orig.mgz $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /Applications/freesurfer Set subject home dir to /Applications/freesurfer/subjects/bert Using interface file /Applications/freesurfer/tktools/tkmedit.tcl Segfault Setting global interpreter xDebug stack (length: 2) 01: main() 01: Setting global interpreter 00: 00: dyn-152-3-184-222:freesurfer joonkoopark$ more .xdebug_tksurfer Segfault Initializing glut xDebug stack (length: 1) 00: 00: Initializing glut Segfault Initializing glut dyn-152-3-184-222:freesurfer joonkoopark$Any idea what went wrong and how to fix it?
Thank you!
Joon
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Zeki
I'm using OSX 10.7.5. And, yes I have installed XQuartz as instructed by the freesurfer installation website.
Thanks!
Joon
-- Joonkoo Park, Ph.D. Postdoctoral Associate Center for Cognitive Neuroscience Duke University http://www.joonkoo.org/
On Thu, Jun 12, 2014 at 11:51 AM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
Hi Joon,
What version of OSX are you on and have you installed XQuartz ( http://xquartz.macosforge.org/landing/)? XQuartz is required for proper tkmedit/tksurfer functionality.
-Zeke
On 06/11/2014 11:48 PM, Joonkoo Park, Ph.D. wrote:
Hello,
I've used FreeSurfer previously on a linux machine (from a previous lab). Now, I have just installed it on a Mac OSX, using the "freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg" version. I followed all the instructions on the installation page. However, there were segfault errors when running both tkmedit and tksurfer as follows:
dyn-152-3-184-222:freesurfer joonkoopark$ more .xdebug_tkmedit tkmedit started: Wed Jun 11 23:28:05 2014 /Applications/freesurfer/tktools/tkmedit.bin bert orig.mgz $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5$ Set user home dir to /Applications/freesurfer Set subject home dir to /Applications/freesurfer/subjects/bert Using interface file /Applications/freesurfer/tktools/tkmedit.tcl
Segfault Setting global interpreter xDebug stack (length: 2) 01: main() 01: Setting global interpreter 00: 00: dyn-152-3-184-222:freesurfer joonkoopark$ more .xdebug_tksurfer Segfault Initializing glut xDebug stack (length: 1) 00: 00: Initializing glut Segfault Initializing glut dyn-152-3-184-222:freesurfer joonkoopark$Any idea what went wrong and how to fix it?
Thank you!
Joon
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Joonkoo Park, Ph.D. -
Z K