Marcos,

Our Centos 4_x86_64 build machine uses kernel v2.6.9-89.33.1, and the
Centos 6_x86_64 machine uses v2.6.32-279.22.1.

Before trying an earlier Fedora, can you try setting this in your tcsh
prior to setting-up freesurfer and running tkmedit?

set anyerror

there was a bug in tcsh 6.17.06 but i think it was fixed in 6.18.
'set anyerror' was the workaround.

Nick

On Sat, 2013-03-09 at 21:15 -0300, Marcos Martins da Silva wrote:
> Hi, Nick. Thank you for your fast answer.
> My tcsh is version 6.18.00-3 (64 bit).
> All are servers here are Fedora. But this machine I am using (a laptop
> for tests) is using the newest version. Perhaps, I can try with a
> previous version. What is the kernel version CentOS 4 or 6 uses?
> 
> Em Sáb, 2013-03-09 às 18:18 -0500, Nick Schmansky escreveu: 
> > Marcos,
> > 
> > Does mri_convert work?  What version of tcsh was installed?  Maybe you
> > can try the freesurfer centos4_x86_64 distribution?  We havent tested on
> > Fedora 18 so we havent seen this before.
> > 
> > Nick
> > 
> > 
> > On Sat, 2013-03-09 at 16:11 -0300, Marcos Martins da Silva wrote:
> > > I did and got the following to test freesurfer installation according
> > > to freesurfer website directions:
> > > [marcos@alien ~]$ tkmedit bert orig.mgz
> > > 
> > > 
> > > ===================================
> > > ERROR: A segfault has occurred. This is not your fault,
> > >   : but is most likely an unrecoverable error and has
> > >   : made the program unstable.
> > >   :
> > >   : Please send the contents of the file .xdebug_tkmedit
> > >   : that should be in this directory to freesurfer@nmr.mgh.harvard.edu
> > >   :
> > >   : Now exiting...
> > >   :
> > > ___________________________________
> > > the contents of .xdebug_tkmedit:
> > > tkmedit started: Sat Mar  9 14:16:07 2013
> > > 
> > >         /usr/local/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 /home/marcos
> > > Set subject home dir to /usr/local/freesurfer/subjects/bert
> > > 
> > > Segfault
> > > Importing volume with MRIread
> > > xDebug stack (length: 5)
> > >           04: Volm_ImportData( this=0x27f84ab0,
> > > isSource=/usr/local/freesurfer/subjects/bert/mri/orig.mgz )
> > >           04: Importing volume with MRIread
> > >         03: LoadVolume( iType=0, isName=orig.mgz, ibConform = 0 )
> > >         03: Reading data into volume
> > >       02: ParseCmdLineArgs( argc=3,
> > > argv=/usr/local/freesurfer/tktools/tkmedit.bin )
> > >       02: Loading volume orig.mgz
> > >     01: main()
> > >     01: Parsing command line arguments
> > >   00: 
> > >   00:
> > > 
> > > ___________________________________
> > > running bugr I got:
> > > FREESURFER_HOME: /usr/local/freesurfer
> > > 
> > > Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0
> > > 
> > > RedHat release: Fedora release 18 (Spherical Cow)
> > > 
> > > Kernel info: Linux 3.8.1-201.fc18.x86_64 x86_64
> > > 
> > > 
> > > ___________________________________
> > > Additional environment info:
> > > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 --------
> > > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> > > FREESURFER_HOME   /usr/local/freesurfer
> > > FSFAST_HOME       /usr/local/freesurfer/fsfast
> > > FSF_OUTPUT_FORMAT nii.gz
> > > SUBJECTS_DIR      /usr/local/freesurfer/subjects
> > > MNI_DIR           /usr/local/freesurfer/mni
> > > 
> > > ___________________________________
> > > [marcos@alien ~]$ which tkmedit
> > > /usr/local/freesurfer/bin/tkmedit
> > > ___________________________________
> > > 
> > > I did the installation according website. My only additional step was
> > > to install tcsh because when I tried tkmedit it returned:
> > > bash: /usr/local/freesurfer/bin/tkmedit: /bin/tcsh: bad interpreter:
> > > File or directory not found.
> > > 
> > > My machine is an Alienware MX17R2 with 8GB RAM and Intel(R) Core(TM)
> > > i5 CPU       M 520  @ 2.40GHz (Quadcore)
> > > My video from lspci is Advanced Micro Devices [AMD] nee ATI Broadway
> > > XT [Mobility Radeon HD 5800 Series] and I am using native drivers
> > > instead of AMD proprietary driver
> > > 
> > > thank you for your support
> > > 
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > 
> > 
> > 
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