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 > > > > > > > > > > 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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer