Thank you very much for your help. The configuration for FreeSurfer is done sucessfully. I have pasted the output during configuration:
[EMAIL PROTECTED] local]# setenv FREESURFER_HOME /usr/local/freesurfer [EMAIL PROTECTED] 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: [EMAIL PROTECTED] local]# tkmedit bert orig.mgz tkmedit: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory [EMAIL PROTECTED] local]# cd freesurfer [EMAIL PROTECTED] freesurfer]# tkmedit bert orig.mgz tkmedit: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory [EMAIL PROTECTED] freesurfer]# I ran the "recon-all -s -bert -all" command and it stopped with the following error message: [EMAIL PROTECTED] 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 <[EMAIL PROTECTED]> 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: > > [EMAIL PROTECTED] ~]# set echo=1 > [EMAIL PROTECTED] ~]# setenv FREESURFER_HOME </usr>/freesurfer > setenv FREESURFER_HOME > [EMAIL PROTECTED] ~]# source $FREESURFER_HOME/SetUpFreeSurfer.csh > source /SetUpFreeSurfer.csh > /SetUpFreeSurfer.csh: No such file or directory. > [EMAIL PROTECTED] ~]# > > 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 <[EMAIL PROTECTED]> 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 > > > > > > > > > > > _______________________________________________ > > 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
