Hello FreeSurfers,<br><br>recon-all -make is working now, but it&#39;s
taking as long as it did the first time I ran it.  I originally ran &quot;recon-all -s cb -i CB_anat+org.BRIK -i CB_anat2+orig.BRIK -all&quot; (for example) back in May and haven&#39;t messed with the results except for generating some label files with mri_annotation2label.  I deleted the original BRIKs, but I don&#39;t see why that would matter in this case since the orig.mgz files are still there.  Is it taking so long because so
much has changed between 4.3 and 4.5, or is something wrong?  <br>
<br>Thanks,<br><br clear="all">Alessandro D. Gagliardi<br>Ph.D. Candidate<br>Integrative Neuroscience Program<br>Rutgers University Mind Brain Analysis<br><a href="mailto:adfgagliardi@gmail.com">adfgagliardi@gmail.com</a><br>

<br>P.S. To generate a2009s annotations files for fsaverage, do I just run &quot;recon-all -s fsaverage -make all&quot;?<br><br><div class="gmail_quote">On Sat, Feb 13, 2010 at 4:28 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;"><div class="im">Hi Alessandro,<br>
<br>
usually that means that the smoothwm is out of date with the sphere.reg. You can run mris_euler_number on both to make sure they have the same number of vertices, faces and edges. Or you can just run<br>
<br>
recon-all -s $subject -make all<br>
<br>
which will rebuild things if it needs to<br></div></blockquote></div>