Gillian,
This tkmedit crash problem is a strange one. Something must have changed, and I’ll try to suggest some things to try.
Was your .cshrc file changed? Anything added to it that might change LD_LIBRARY_PATH s?
What is the output if you run:
otool -L `which tkmedit.bin`
it should be something like this (although my system is 10.9.3, Mavericks): /Applications/freesurfer/tktools/tkmedit.bin: /usr/pubsw/packages/tcltktixblt/current/lib/libtk8.4.dylib (compatibility version 8.4.0, current version 8.4.0) /usr/pubsw/packages/tcltktixblt/current/lib/libtcl8.4.dylib (compatibility version 8.4.0, current version 8.4.0) /opt/X11/lib/libGLU.1.dylib (compatibility version 1.3.0, current version 1.3.0) /opt/X11/lib/libGL.1.dylib (compatibility version 1.2.0, current version 1.2.0) /opt/X11/lib/libX11.6.dylib (compatibility version 10.0.0, current version 10.0.0) /opt/X11/lib/libXmu.6.dylib (compatibility version 9.0.0, current version 9.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 125.2.11) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.9.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 830.0.0)
did any of the files in /opt/X11 change recently?
Did you recently update XQuartz? what version are you using? I use v2.7.5. open Applications/Utilities/XQuartz to find out. I just now opened XQuartz and see that it is prompting me to upgrade to 2.7.6 and also that there is a checkbox to ‘Automatically download and install updates in the future’. Perhaps that was set for you (if you suddenly have version 2.7.6). If so, go to the XQuartz site and get v2.7.5. Although after I updated to v2.7.6, tkmedit still works for me, but I’m using Mavericks.
Can you try creating a new user account and try freesurfer using that? perhaps some config thing happened in your regular account.
Lastly, if all else fails, I’d suggest removing Freesurfer and XQuartz and reinstalling. Perhaps some files got corrupted on the disk.
Nick
---------- Forwarded message ---------- Date: Fri, 30 May 2014 16:32:11 +0000 From: "Cooke, Gillian" gcooke@illinois.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Seg fault
It is happening with all subjects that I've loaded this week, but this is my second pass through checks on this data - so all have previously loaded successfully.
On May 30, 2014, at 11:24 AM, Douglas N Greve wrote:
It might be the data you are trying to load in. Does it happen with other subjects or volumes?
On 05/30/2014 12:17 PM, Cooke, Gillian wrote:
Thanks for the quick responses. I'm using version 10.7.5 - I purposely haven't updated this as we've been analysing a large set of intervention data. I'm also using freesurfer-Darwin-lion-stable-pub-v5.3.0 - again we've been consistent with this and have run everything in this version. I'm still using the same machine, I'm writing to a large server so there is plenty of space. The only updates I've installed since I last used Freesurfer successfully are safari and iTunes, and I was getting this error before that installation.
On May 30, 2014, at 11:04 AM, Bruce Fischl wrote:
Hi Gillian
what changed? Did you upgrade a video driver? Use a new machine? Update the operating system? Run out of disk space? Something is different....
Bruce On Fri, 30 May 2014, Cooke, Gillian wrote:
Hi, I've been working with Freesurfer for years and have suddenly been getting this fault: tkmedit started: Fri May 30 10:08:23 2014 /Applications/freesurfer/tktools/tkmedit.bin ACCE633_1 brainmask.mgz -aux T1.mgz -surfs $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /Users/gilliancooke Set subject home dir to /Volumes/HealthAging/ACCE/Freesurfer/ACCE633_1 Using interface file /Applications/freesurfer/tktools/tkmedit.tcl Segfault Setting global interpreter xDebug stack (length: 2) 01: main() 01: Setting global interpreter 00:Z K zkaufman@nmr.mgh.harvard.edu 00: Any suggestions? Many thanks, Gill _____________________ Gillian Cooke, Ph.D. Postdoctoral Research Associate Lifelong Brain & Cognition Lab Beckman Institute University of Illinois, Urbana
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
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Nick Schmansky, MGH