Did you try running the freesurfer CentOS6 version on the upgraded
version of Fedora?

-Zeke

On 04/03/2013 08:09 AM, Sidy Fall wrote:
> After doing an upgrade from fedora 17 to fedora 18,I am trying to
> execute the installation tests, I can't start "$tkmedit", tksurfer or
> mri_convert. But freeview and qdec seem to be good.
> Tested with a CentOS4 or a CentOS6
> recon-all,v 1.379.2.65 2013/02/19 22:34:56 nicks Exp $
> -------- freesurfer-Linux-centos4_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
> FSL_DIR           /usr/local/fsl
> ---------
> Linux version 3.8.5-201.fc18.x86_64 (mockbuild@bkernel02) (gcc version
> 4.7.2 20121109 (Red Hat 4.7.2-8))
> processor:Intel(R) Core(TM)2 Duo CPU     E8500  @ 3.16GHz
> tcsh 6.18.00 (Astron) 2012-01-14
> --------------------
> When I do: tkmedit bert orig.mgz,
> it returned,
> 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

> <mailto:freesurfer@nmr.mgh.harvard.edu>

>    :
>    : Now exiting...
>    :
> -----------------------
> When I do: tksurfer bert rh pial,
> it returned,
> subject is bert
> hemi    is rh
> surface is pial
> surfer: current subjects dir: /usr/local/freesurfer/subjects
> surfer: not in "scripts" dir ==> using cwd for session root
> surfer: session root data dir ($session) set to:
> surfer:     /home/fallsi/Protocoles
> checking for nofix files in 'pial'
> Reading image info (/usr/local/freesurfer/subjects/bert)
> Reading /usr/local/freesurfer/subjects/bert/mri/orig.mgz
> surfer: Reading header info from
> /usr/local/freesurfer/subjects/bert/mri/orig.mgz
>
> -------------------
> When I start mri_convert, I have this error message:
> mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from IM1...
> Segmentation fault (core dumped)
> ---------------
> the contents of .xdebug_tkmedit:
>   tkmedit started: Wed Apr  3 11:43:32 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/fallsi/Protocoles
> Set subject home dir to /usr/local/freesurfer/subjects/bert
>
> Segfault
> Importing volume with MRIread
> xDebug stack (length: 5)
>            04: Volm_ImportData( this=0x27675600,
> 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:
> ----------------------
> Thank you in advance,
>
>

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