Hi Bruce and Pedro,<br><br>Thank you both for sending me your suggestions.  <br>Just to let you know, because my .dcm (dicom) files had a space and two dots in the filenames:<br>(e.g. &quot;2008_12_08.ek -0035-0001-00001.dcm&quot; )<br>
(and using quotes around the file name or &quot;\ &quot; within the filename without the quotes did not work with recon-all), recon-all truncated the filename before the space as &quot;2008_12_08.ek&quot; feeding it to an mri_convert command and gave an error message.<br>
<br>So I worked around this problem as follows: I converted the .dcm series to a nifti .nii volume using 3D Slicer, and then used mri_convert to convert the .nii format to .mgz format.  Then I ran recon-all on the .mgz formatted file and it is now running successfully. <br>
<br>I see on the online tutorials and slides, that this process takes about 20 hours. Is there a way to only run partial steps pertaining only to the cortical thickness?  <br><br>Pedro also suggested that I go through the FreeSurferBeginnersGuide wiki which I am doing now.  <br>
<br>Also, reading some mailing lists emails, I noticed that matlab can be used to analyze the cortical thickness statistiics, and also freesurfer comes with matlab scripts.  I will try these tools out as well.<br><br>Thank you for your time,<br>
John<br><br><div class="gmail_quote">On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl <span dir="ltr">&lt;<a href="mailto:fischl@nmr.mgh.harvard.edu">fischl@nmr.mgh.harvard.edu</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
recon-all \<br>
        -i &lt;one slice in the anatomical dicom series&gt; \<br>
        -s &lt;subject id that you make up&gt; \<br>
        -sd &lt;directory to put the subject folder in&gt; \<br>
        -all<br>
<br>
<br>
cheers<br><font color="#888888">
Bruce</font><div><div></div><div class="h5"><br>
<br>
<br>
On Tue, 5 Jul 2011, John Drozd wrote:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
I am running freesurfer on 64 bit Fedora 10 linux.<br>
I am using version:  freesurfer-Linux-centos4_x86_<u></u>64-stable-pub-v4.3.0.<br>
Can anyone point me to a reference web page listing what steps I need to<br>
type to process<br>
a series of MRI dicom slices and use FreeSurfer to measure cortical<br>
thickness for this dicom series?<br>
<br>
Thank you,<br>
John<br>
<br>
--<br>
John Drozd<br>
Post-Doctoral Fellow, Robarts Research Institute<br>
The University of Western Ontario<br>
London, ON, Canada<br>
<a href="http://publish.uwo.ca/%7Ejdrozd2/index.htm" target="_blank">http://publish.uwo.ca/~<u></u>jdrozd2/index.htm</a><br>
 <br>
<br>
<br>
</blockquote>
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<div>The University of Western Ontario</div>
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