you will need to use the rh9 freesurfer distribution on rhel3, since rhel3 appears not to contain libstdc++.so.6. also, you will need to install libglut, as it appears to not be installed on your system.
On Wed, 2006-04-26 at 16:01 -0500, Binu Thomas wrote:
Thank you very much for your help. The configuration for FreeSurfer is done sucessfully. I have pasted the output during configuration:
[root@localhost local]# setenv FREESURFER_HOME /usr/local/freesurfer [root@localhost local]# source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Linux-centos4-stable-pub-v3.0.2 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast SUBJECTS_DIR /usr/local/freesurfer/subjects FUNCTIONALS_DIR /usr/local/freesurfer/sessions MINC_BIN_DIR /usr/local/freesurfer/mni/bin MINC_LIB_DIR /usr/local/freesurfer/mni/lib PERL5LIB /usr/local/freesurfer/mni/lib/perl5/5.8.0 GSL_DIR /usr/local/freesurfer/lib/gsl QTDIR /usr/local/freesurfer/lib/qt TCLLIBPATH /usr/local/freesurfer/lib/tcltktixblt/lib FSL_DIR /usr/local/freesurfer/fsl
Now, I am having trouble with testing the software: I tried the first few commands on the Testing FreeSurfer page and here is the error I get:
[root@localhost local]# tkmedit bert orig.mgz tkmedit: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory [root@localhost local]# cd freesurfer [root@localhost freesurfer]# tkmedit bert orig.mgz tkmedit: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory [root@localhost freesurfer]#
I ran the "recon-all -s -bert -all" command and it stopped with the following error message:
#@# Skull Stripping Wed Apr 26 15:40:43 CDT 2006 /usr/local/freesurfer/subjects/bert/mri
mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz T1.mgz brainmask.auto.mgz mri_watershed: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory Linux localhost.localdomain 2.4.21-40.ELsmp #1 SMP Thu Feb 2 22:22:39 EST 2006 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Wed Apr 26 15:40:43 CDT 2006
I am installing the CentOS4 stable version of FreeSurfer on Red Hat Ent. Linux 3. Can this be a problem? Thanks again for any help possible, Binu.
Binu Thomas, M.S. Computer Programmer III Department of Psychiatry UT Southwestern Medical Center Phone: 214-645-2792
Nick Schmansky nicks@nmr.mgh.harvard.edu 04/26/06 11:53 AM >>>
Remove the angle brackets from the pathname, that is, the < and > chars. In Unix, these are the redirection commands, and not valid pathname characters.
So, type this:
setenv FREESURFER_HOME /usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh
On Wed, 2006-04-26 at 11:42 -0500, Binu Thomas wrote:
Thanks for the reply! Here is a detail of all that I did. I downloaded the RH9 version of the software to my /usr/local directory and
installed
it with the "tar xzvf" command. I then changed the shell to tcsh and then the rest of the output is as follows:
[root@localhost ~]# set echo=1 [root@localhost ~]# setenv FREESURFER_HOME </usr>/freesurfer setenv FREESURFER_HOME [root@localhost ~]# source $FREESURFER_HOME/SetUpFreeSurfer.csh source /SetUpFreeSurfer.csh /SetUpFreeSurfer.csh: No such file or directory. [root@localhost ~]#
I have followed all instructions provided on the freesurfer website.
Thanks in advance for the help, Binu.
Binu Thomas, M.S. Computer Programmer III Department of Psychiatry UT Southwestern Medical Center Phone: 214-645-2792
Nick Schmansky nicks@nmr.mgh.harvard.edu 04/26/06 11:33 AM >>>
Also, try enabling command echoing first, like this:
set echo=1 source $FREESURFER_HOME/SetUpFreeSurfer.csh
this will print-out details of the script as it runs.
On Wed, 2006-04-26 at 12:27 -0400, Bruce Fischl wrote:
Hi Binu,
can you send us the complete screen output from what you tried?
thanks, Bruce On Wed, 26 Apr 2006, Binu Thomas wrote:
Dear all, I posted a message yesterday regarding the same problem, didn't get much help, hoping to get some help today. I am running
Red
Hat Enterprise Linux 3, tried to install Freesurfer CentOS4, when
I
try
to access the SetUpFreeSurfer.csh file with the "source" command,
I
get
the error: File or Directory not found. I had the feeling that
CentOS4
version of FreeSurfer might not be compatible with my OS, so I
tried
to
configure the RH9 version of the software and ended up with the
same
error. I can see that the file exists in the "freesurfer" folder.
I
would greatly appreciate any help.
Thanks in advance, Binu Thomas. Univ. of TX Southwestern Medical Center. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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