Fatima,<div><br></div><div>Try this simple procedure to get started.</div><div><br></div><div>1) Convert your dicom files to 001.mgz</div><div>recon-all -i DICOM_FILE_DIR -o 001.mgz</div><div><br></div><div>2) Inside your subjects_dir create a subdirectory like this:</div>

<div>mkdir -p $SUBJECTS_DIR/test01/mri/orig</div><div><br></div><div>3) copy your 001.mgz into that dir</div><div>cp 001.mgz $SUBJECTS_DIR/test01/mri/orig</div><div><br></div><div>4) run recon-all</div><div>recon-all -s test01 -all</div>

<div><br></div><div>Hope it helps</div><div><br></div><div>PPJ</div><div><br></div><div><br clear="all">-----------------------------------------------------------<br>Pedro Paulo de M. Oliveira Junior<br>Diretor de Operaçőes<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;">








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<div>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 </div>
<div>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</div>
<div>one acquisition) to create the orig.mgz file. however, when I try and run the following command:</div>
<div> </div>
<div>&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:</div>
<div> </div>
<div>[fsl@localhost DicomImages]$ recon-all -i CON_ADAMS_MONIQUE/orig.mgz -autorecon1 -s CON_ADAMS_MONIQUE</div>
<div>ERROR: cannot find CON_ADAMS_MONIQUE/orig.mgz</div>
<div>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</div>
<div> </div>
<div>recon-all exited with ERRORS at Wed Jun 17 08:59:47 BST 2009</div>
<div> </div>
<div> </div>
<div>Please can you advise me on what the problem is and how to correct it? </div>
<div> </div>
<div>Thank you. </div>
<div> </div>
<div>Fatima</div>
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<div> </div>
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