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" <gco...@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 <zkauf...@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
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>>>>> but does not contain patient information, please contact the sender and
>>>>> properly
>>>>> dispose of the e-mail.
>>>>
>>>> _______________________________________________
>>>> Freesurfer mailing list
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>>>>
>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@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
>>
>>
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>>
>>
>>
>>
>>
>
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