Sorry. I mistyped the first command<div><br></div><div>(Wrong) recon-all -i DICOM_FILE_DIR -o 001.mgz</div><div><br></div><div>(Correct) mri_convert -i DICOM_FILE_DIR -o 001.mgz<br clear="all">-----------------------------------------------------------<br>

Pedro Paulo de M. Oliveira Junior<br>Diretor de Operações<br>Netfilter &amp; SpeedComm Telecom<br>--- Novo Netfilter 3.0 <a href="http://www.Netfilter.com.br">www.Netfilter.com.br</a><br><br>
<br><br><div class="gmail_quote">2009/6/17 Ahmed, F, Me &lt;<a href="mailto:fahmed@sun.ac.za">fahmed@sun.ac.za</a>&gt; <span dir="ltr">&lt;<a href="mailto:fahmed@sun.ac.za">fahmed@sun.ac.za</a>&gt;</span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">











<div lang="EN-ZA" link="blue" vlink="purple">

<div>

<p><span style="font-size:11.0pt;color:#1F497D">PPJ,</span></p>

<p><span style="font-size:11.0pt;color:#1F497D"> </span></p>

<p><span style="font-size:11.0pt;color:#1F497D">Thank you for your response, I tried your procedure and got the following
message: </span></p>

<p><span style="font-size:11.0pt;color:#1F497D"> </span></p>

<p><span style="font-size:11.0pt;color:#1F497D">[fsl@localhost CON_ADAMS_MONIQUE]$ cp 001.mgz
$SUBJECTS_DIR/CON_ADAMS_MONIQUE/mri/orig</span></p>

<p><span style="font-size:11.0pt;color:#1F497D">cp: cannot stat `001.mgz&#39;: No such file or directory</span></p>

<p><span style="font-size:11.0pt;color:#1F497D"> </span></p>

<p><span style="font-size:11.0pt;color:#1F497D">I don’t know why that happens. </span></p>

<p><span style="font-size:11.0pt;color:#1F497D"> </span></p>

<p><span style="font-size:11.0pt;color:#1F497D"> </span></p>

<p><span style="font-size:11.0pt;color:#1F497D"> </span></p>

<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">

<p><b><span lang="EN-US" style="font-size:10.0pt">From:</span></b><span lang="EN-US" style="font-size:10.0pt"> <a href="mailto:freesurfer-bounces@nmr.mgh.harvard.edu" target="_blank">freesurfer-bounces@nmr.mgh.harvard.edu</a>
[mailto:<a href="mailto:freesurfer-bounces@nmr.mgh.harvard.edu" target="_blank">freesurfer-bounces@nmr.mgh.harvard.edu</a>] <b>On Behalf Of </b>Pedro Paulo
de Magalhães Oliveira Junior<br>
<b>Sent:</b> 17 June 2009 15:14<br>
<b>To:</b> Ahmed, F, Me<br>
<b>Cc:</b> <a href="mailto:freesurfer@nmr.mgh.harvard.edu" target="_blank">freesurfer@nmr.mgh.harvard.edu</a><br>
<b>Subject:</b> Re: [Freesurfer] error message</span></p>

</div><div><div></div><div class="h5">

<p> </p>

<p>Fatima,</p>

<div>

<p> </p>

</div>

<div>

<p>Try this simple procedure to get started.</p>

</div>

<div>

<p> </p>

</div>

<div>

<p>1) Convert your dicom files to 001.mgz</p>

</div>

<div>

<p>recon-all -i DICOM_FILE_DIR -o 001.mgz</p>

</div>

<div>

<p> </p>

</div>

<div>

<p>2) Inside your subjects_dir create a subdirectory
like this:</p>

</div>

<div>

<p>mkdir -p $SUBJECTS_DIR/test01/mri/orig</p>

</div>

<div>

<p> </p>

</div>

<div>

<p>3) copy your 001.mgz into that dir</p>

</div>

<div>

<p>cp 001.mgz $SUBJECTS_DIR/test01/mri/orig</p>

</div>

<div>

<p> </p>

</div>

<div>

<p>4) run recon-all</p>

</div>

<div>

<p>recon-all -s test01 -all</p>

</div>

<div>

<p> </p>

</div>

<div>

<p>Hope it helps</p>

</div>

<div>

<p> </p>

</div>

<div>

<p>PPJ</p>

</div>

<div>

<p> </p>

</div>

<div>

<p style="margin-bottom:12.0pt"><br clear="all">
-----------------------------------------------------------<br>
Pedro Paulo de M. Oliveira Junior<br>
Diretor de Operações<br>
Netfilter &amp; SpeedComm Telecom<br>
--- Novo Netfilter 3.0 <a href="http://www.Netfilter.com.br" target="_blank">www.Netfilter.com.br</a><br>
<br>
<br>
</p>

<div>

<p>2009/6/17 Ahmed, F, Me &lt;<a href="mailto:fahmed@sun.ac.za" target="_blank">fahmed@sun.ac.za</a>&gt;
&lt;<a href="mailto:fahmed@sun.ac.za" target="_blank">fahmed@sun.ac.za</a>&gt;</p>

<div>

<div>

<p><span style="font-size:10.0pt">Hello,
I am new to using Freesurfer and am trying to run the recon-all stages in order
to get thickness values for brain regions. I have correctly </span></p>

</div>

<div>

<p><span style="font-size:10.0pt">converted
all my dicom images into the correct mgz format as instructed by your manual
and have carried out motion correction (even though I only have</span></p>

</div>

<div>

<p><span style="font-size:10.0pt">one
acquisition) to create the orig.mgz file. however, when I try and run the
following command:</span></p>

</div>

<div>

<p><span style="font-size:10.0pt"> </span></p>

</div>

<div>

<p><span style="font-size:10.0pt">&quot;recon-all
-i &lt;in volume 1&gt; -i &lt;in volume 2&gt; -i &lt;in volume 3&gt;
-autorecon1 -s bert&quot; using my subject name, I get the following error
message:</span></p>

</div>

<div>

<p><span style="font-size:10.0pt"> </span></p>

</div>

<div>

<p><span style="font-size:10.0pt">[fsl@localhost
DicomImages]$ recon-all -i CON_ADAMS_MONIQUE/orig.mgz -autorecon1 -s
CON_ADAMS_MONIQUE</span></p>

</div>

<div>

<p><span style="font-size:10.0pt">ERROR:
cannot find CON_ADAMS_MONIQUE/orig.mgz</span></p>

</div>

<div>

<p><span style="font-size:10.0pt">Linux
localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686
i686 i386 GNU/Linux</span></p>

</div>

<div>

<p><span style="font-size:10.0pt"> </span></p>

</div>

<div>

<p><span style="font-size:10.0pt">recon-all
exited with ERRORS at Wed Jun 17 08:59:47 BST 2009</span></p>

</div>

<div>

<p><span style="font-size:10.0pt"> </span></p>

</div>

<div>

<p><span style="font-size:10.0pt"> </span></p>

</div>

<div>

<p><span style="font-size:10.0pt">Please
can you advise me on what the problem is and how to correct it? </span></p>

</div>

<div>

<p><span style="font-size:10.0pt"> </span></p>

</div>

<div>

<p><span style="font-size:10.0pt">Thank
you. </span></p>

</div>

<div>

<p><span style="font-size:10.0pt"> </span></p>

</div>

<div>

<p><span style="font-size:10.0pt">Fatima</span></p>

</div>

<div>

<p><span style="font-size:10.0pt"> </span></p>

</div>

<div>

<p><span style="font-size:10.0pt"> </span></p>

</div>

</div>

<p><br>
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</div>

<p> </p>

</div>

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

</div>


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