Dear Pedro,<div><br></div><div>I would like to start with the tutorials but I don&#39;t have permission to copy the data to the subjects directory, how I can change this?</div><div><br></div><div>Best regards,</div><div><br>
</div><div>Carolina</div><div><div><br><div class="gmail_quote">2011/2/22 Pedro Paulo de Magalhăes Oliveira Junior <span dir="ltr">&lt;<a href="mailto:ppj@netfilter.com.br">ppj@netfilter.com.br</a>&gt;</span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
try the command:<div><br></div><div>sudo apt-get install tcl</div><div><br></div><div>-- PPJ</div><div><br>
Please: cc the freesurfer list when answering<br><br><div class="gmail_quote">2011/2/22 Carolina Valencia <span dir="ltr">&lt;<a href="mailto:cvalencia@linkdx.com.co" target="_blank">cvalencia@linkdx.com.co</a>&gt;</span><div>
<div></div><div class="h5"><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">

Hi Pedro,<div><br><div>Finally, I could install it with the license file and the environment is properly set without warnings. </div><div>But trying to test it, following the instruction on the wiki page I have a problem</div>



<div><br></div><div><div>cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit bert orig.mgz</div><div>/usr/local/freesurfer/bin/tcl_setup: No existe el fichero o el directorio.</div></div><div><br></div><div>in the .bashrc I copy the right location of the freesurfer folder</div>



<div><div>FREESURFER_HOME=/home/cvalencia/freesurfer</div><div><div>source $FREESURFER_HOME/SetUpFreeSurfer.sh</div></div></div><div><br><div><div></div><div><br><div class="gmail_quote">2011/2/21 Pedro Paulo de Magalhăes Oliveira Junior <span dir="ltr">&lt;<a href="mailto:ppj@netfilter.com.br" target="_blank">ppj@netfilter.com.br</a>&gt;</span><br>



<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">run this command<div><br></div><div><font face="&#39;courier new&#39;, monospace">sudo</font> <span style="font-family:monospace;white-space:pre-wrap;font-size:medium">rm -rf $FREESURFER_HOME</span><div>



<div></div><div><br>


<br><br><div class="gmail_quote">2011/2/21 Carolina Valencia <span dir="ltr">&lt;<a href="mailto:cvalencia@linkdx.com.co" target="_blank">cvalencia@linkdx.com.co</a>&gt;</span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">





Thanks Pedro,<div><br><div>How I uninstall that version to re-install the correct version?</div><div>I look for some answers and try </div><div><br></div><div><span style="font-family:monospace;white-space:pre-wrap;font-size:medium">rm -rf $FREESURFER_HOME</span></div>






<div><font face="monospace" size="3"><span style="white-space:pre-wrap"><br></span></font></div>It says that I don&#39;t have permission,how I can unistall it, if i&#39;m the admin user?<div>
<font face="monospace" size="3"><span style="white-space:pre-wrap"><br></span></font>Thanks in advance,</div>
<div><br></div><font color="#888888"><div>Carolina</div></font><div><div><div></div><div><br><div class="gmail_quote">2011/2/21 Pedro Paulo de Magalhăes Oliveira Junior <span dir="ltr">&lt;<a href="mailto:ppj@netfilter.com.br" target="_blank">ppj@netfilter.com.br</a>&gt;</span><br>





<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS<div><br></div><div><br><div class="gmail_quote">2011/2/21 Carolina Valencia <span dir="ltr">&lt;<a href="mailto:cvalencia@linkdx.com.co" target="_blank">cvalencia@linkdx.com.co</a>&gt;</span><div>






<div></div><div><br>

<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux<div>








<br></div><div>Thanks,</div><div><br><div><br><div class="gmail_quote">2011/2/21 Pedro Paulo de Magalhăes Oliveira Junior <span dir="ltr">&lt;<a href="mailto:ppj@netfilter.com.br" target="_blank">ppj@netfilter.com.br</a>&gt;</span><div>








<div></div><div><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Please send the result of the command:<div><br></div><div><font face="&#39;courier new&#39;, monospace">uname -a</font><div>









<div></div><div><br><br><div class="gmail_quote">On Mon, Feb 21, 2011 at 10:31, Carolina Valencia <span dir="ltr">&lt;<a href="mailto:cvalencia@linkdx.com.co" target="_blank">cvalencia@linkdx.com.co</a>&gt;</span> wrote:<br>











<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Bruce,<div><br><div>I&#39;m experimenting problems with the installation on Ubuntu too.</div><div>There&#39;s is warning in the welcome message, it seems that something is missing: </div>











<div><br></div><div><div>-------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 --------</div>
<div>Setting up environment for FreeSurfer/FS-FAST (and FSL)</div><div>WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist</div><div>FREESURFER_HOME   /home/cvalencia/Descargas/freesurfer</div><div>FSFAST_HOME       /home/cvalencia/Descargas/freesurfer/fsfast</div>












<div>FSF_OUTPUT_FORMAT nii</div><div>SUBJECTS_DIR      /home/cvalencia/Descargas/freesurfer/subjects</div><div>MNI_DIR           /home/cvalencia/Descargas/freesurfer/mni</div><div>FSL_DIR           /usr/share/fsl/4.1</div>












</div><div><br></div><div><br></div><div>I try to test it and it shows</div><div><div>cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit</div><div>/home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de ejecutable incorrecto. Binary file not executable.</div>












<div><br></div><div>Thanks a lot,</div><div><br></div><div>Carolina</div><br><div class="gmail_quote">2011/2/18 Bruce Fischl <span dir="ltr">&lt;<a href="mailto:fischl@nmr.mgh.harvard.edu" target="_blank">fischl@nmr.mgh.harvard.edu</a>&gt;</span><br>












<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Jie,<br>
<br>
what hardware are you using? Is it a 64 bit operating system?<br>
<br>
cheers<br><font color="#888888">
Bruce</font><div><div></div><div><br>
On Sat, 19 Feb 2011, Liukarl wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
Hello, Freesurfer experts:<br>
<br>
<br>
<br>
I am new to freesurfer and try to<br>
install the newest version of freesurfer in Ubuntu system. I closely<br>
followed the instructions, and the only difference is that I<br>
installed it in my Documents, instead of local folder.<br>
<br>
<br>
<br>
Below is the output after “source<br>
$FREESURFER_HOME/SetUpFreeSurfer.sh”<br>
<br>
<br>
<br>
--------<br>
freesurfer-Linux-centos4-stable-pub-v5.0.0 --------<br>
<br>
Setting up environment for<br>
FreeSurfer/FS-FAST (and FSL)<br>
<br>
FREESURFER_HOME<br>
/home/jie/Documents/freesurfer/<br>
<br>
FSFAST_HOME<br>
/home/jie/Documents/freesurfer//fsfast<br>
<br>
FSF_OUTPUT_FORMAT nii<br>
<br>
SUBJECTS_DIR<br>
/home/jie/Documents/freesurfer//subjects<br>
<br>
MNI_DIR<br>
/home/jie/Documents/freesurfer//mni<br>
<br>
<br>
<br>
<br>
Everything seems fine and I also added<br>
the .license file to the freesurfer folder.<br>
<br>
<br>
<br>
But when I test it by “tkmedit bert<br>
orig.mgz”, it reponds “Illegal instruction”<br>
<br>
<br>
<br>
If I type in “recon-all”, it will<br>
show<br>
<br>
“ Required Arguments:<br>
<br>
  -subjid &lt;subjid&gt;<br>
<br>
  -&lt;process directive&gt;…...<br>
”<br>
and the other arguments.<br>
<br>
<br>
<br>
How to fix the problem and make<br>
Fressurfer run? Any help is appreciated. Thanks a lot!<br>
<br>
<br>
<br>
Jie<br>
</blockquote>
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</blockquote></div></div></div><br><br>
</div></div>
</blockquote></div></div></div><br></div>
</blockquote></div><br><br clear="all"><br></div></div>-- <br>
</div></div>
</blockquote></div><br></div></div></div>
</blockquote></div><br><br clear="all"><br></div></div>--<br>
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</blockquote></div></div></div><br></div>
</blockquote></div><br><br>
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