Pietro<div><br></div><div>You should first import your *.dcm files with the command</div><div><br></div><div>recon-all -i first_dicom_image_name.dcm -s subjID </div><div><br></div><div>Then when you process your data you would type</div>

<div><br></div><div>recon-all -s subjID -autorecon1 -autorecon2 </div><div><br></div><div>or whatever steps you are using.</div><div><br></div><div>Darren<br><br><div class="gmail_quote">On Wed, Sep 26, 2012 at 9:33 AM, pietro de rossi <span dir="ltr">&lt;<a href="mailto:derossi05@gmail.com" target="_blank">derossi05@gmail.com</a>&gt;</span> wrote:<br>

<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">



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Dear FreeSurfers,
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<div>I am a beginner, trying to process some 3T MPRAGE scans on my own for a project.<br>
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<div>I have a couple of simple questions</div>
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<ol style="font-family:Calibri;font-size:medium">
<li><font face="Calibri,Verdana,Helvetica,Arial"><span style="font-size:11pt">When I run the recon-all –autorecon1 –autorecon2 command it asks me for 001.mgz in mri/orig so I copy and paste the volume into the folder and the command works. My question is: do
 I need to change 001.mgz to 002, 003 an so on for every scan I process?</span></font>
</li><li><font face="Calibri,Verdana,Helvetica,Arial"><span style="font-size:11pt">I have to process 3T scans in a .dcm format. Can I just process the scan as it is? Do I have to save the .dcm files as another format, maybe a .mnc file?</span></font>
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<div><font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size:15px">thank you very much in advance,</span></font></div>
<div><font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size:15px"><br>
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<div><font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size:15px">Pietro</span></font></div><span class="HOEnZb"><font color="#888888">
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<div style="font-family:arial,sans-serif"><span><font color="#222222">Pietro De Rossi</font></span>, MD</div>
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<span style="font-size:10pt;font-family:&#39;Arial Narrow&#39;">Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant&#39;Andrea, Via di Grottarossa 1035-1039, 00189 Roma<br>


</span><span lang="EN-GB" style="font-size:6.5pt;font-family:&#39;Arial Narrow&#39;"><br>
</span><span lang="EN-GB" style="font-size:10pt;font-family:&#39;Arial Narrow&#39;">NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189
 Rome, Italy</span></div>
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Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA</span><br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br>Darren Gitelman, MD<br>Northwestern University<br>710 N. Lake Shore Dr.<br>Abbott 11th Floor<br>Chicago, IL 60611<br>Ph: (312) 908-8614<br>Fax: (312) 908-5073<br>

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