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...
:
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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:
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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
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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
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[marcos@alien ~]$ which tkmedit
/usr/local/freesurfer/bin/tkmedit
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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