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 _______________________________________________ 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.
