Hi Ian, Thanks for the information. So I followed your instructions carefully with the same result (I modified the terminal options as well). I also modified it as well to see if I can get it working but to no avail. Here is the contents of my .tcshrc file:
#.tcshrc
# User specific aliases and functions
alias rm 'rm -i' alias cp 'cp -i' alias mv 'mv -i' alias freesurfer 'setenv FREESURFER_HOME /usr/local/freesurfer; setenv SUBJECTS_DIR /usr/local/freesurfer/subjects; source $FREESURFER_HOME/SetUpFreeSurfer.csh'
set prompt='[%n@%m %c]# '
setenv FREESURFER_HOME /usr/local/freesurfer setenv SUBJECTS_DIR /usr/local/freesurfer/subjects source $FREESURFER_HOME/SetUpFreeSurfer.csh
Here is what my terminal looks like: Which looks correct to me....
-------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- 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 [root@brian-Latitude-E6410 ~]# tkmedit bert config.mgz /usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary file not executable.
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Ian Charest [Ian.Charest@mrc-cbu.cam.ac.uk] Sent: December-30-11 7:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer & Ubuntu 11.10
Hi Brian
I had to change the terminal config for it to use tcsh.
I think Ubuntu now uses The Debian Almquist shell (dash) and I have had problems running freesurfer from it.
install tcsh using aptitude and then in the preferences of your terminal (Edit > profile preferences) in the tab "title and command" click on "run custom command instead of my shell" and type /bin/tcsh as your custom command.
You can also set up some environment variables by editing the .tcshrc found in your home directory.
gedit ~/.tcshrc
and add a modified version of this code according to where your freesurfer install is and where your subject directory lies...
alias freesurfer 'setenv FREESURFER_HOME /usr/local/freesurfer; setenv SUBJECTS_DIR ~/subjects; source $FREESURFER_HOME/SetUpFreeSurfer.csh'
now if you close your terminal and open a new one, freesurfer should work.
Hope it helps
Ian
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of James, Brian [Brian.James@nbrhc.on.ca] Sent: 30 December 2011 20:40 To: martijnsteenwijk@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer & Ubuntu 11.10
That is what I did…my path is /usr/local/freesurfer
However, mine doesn’t seem to work.
Brian.
From: Martijn Steenwijk [mailto:martijnsteenwijk@gmail.com] Sent: December-30-11 2:37 PM To: James, Brian Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] FreeSurfer & Ubuntu 11.10
Just untarring the .tar.gz in /usr/local like documented here (http://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall) works like a charm on Ubuntu 11.10.
Best, Martijn
Van: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens James, Brian Verzonden: vrijdag 30 december 2011 21:13 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: [Freesurfer] FreeSurfer & Ubuntu 11.10
Hi Everyone, I thought I would try installing FreeSurfer on Ubuntu because I was having so many issues trying to install Octave on CentOS. On the bright side, Ubuntu can download Octave directly from the repository. The downside is when I test my freesurfer install with tkmedit bert orig,mgz, I get the following error:
/usr/local/freesurfer/tktools/tksurfer.bin: Exec format error. Binary file not executable.
Is there is something additional I need to install because it is on Ubuntu?
Brian James Technical Applications Analyst North Bay Regional Health Centrehttp://www.nbrhc.on.ca/ (705) 474-8600 x2611
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