Thanks for the fast reply. I have uploaded the entire subject directory and would appreciate if you could take a look.<br><br>/Nikolas<br><br><div class="gmail_quote">On Tue, Feb 1, 2011 at 3:17 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;">Hi Nikolas<br>
<br>
the spiked by themselves aren&#39;t a problem, it&#39;s only if the surface isn&#39;t accurately following the true gray/white boundary that you need to intervene. It&#39;s a bit hard to tell in this case without being able to scroll back and forth, but I suspect the segmentation is a bit inaccurate in this region, which results in an incorrectly fixed topological defect. If you want to, you can tar and gzip the entire subject dir and ftp it for us and I&#39;ll take a look.<br>

<br>
cheers<br>
Bruce<div><div></div><div class="h5"><br>
<br>
On Tue, 1 Feb 2011, Nikolas Borrel-Jensen 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 everybody.<br>
<br>
I have done all the auto-recon steps on my data, and I have some questions<br>
about the quality of the resulting images. I am aware of the troubleshooting<br>
tutorials, but I don&#39;t think these are covering my questions.<br>
<br>
I have uploaded some images of the surfaces and segmentations of a subject<br>
to <a href="http://freesurfer.nikolasborrel.com" target="_blank">http://freesurfer.nikolasborrel.com</a>, and my question is about the spikes<br>
in the inflated surfaces. I have selected two spikes on the surface (green<br>
mark), one for each hemisphere, and have found the corresponding location in<br>
tkmedit in each of the three directions (s,h,c).<br>
<br>
For the spike in the left hemisphere (spike1_lh), I can&#39;t see what should be<br>
causing the spike. The segmentation looks correct.<br>
<br>
For the spike in the right hemisphere (spike_rh), it seems like there are<br>
many &#39;isles of segmentations, but are these causing the spike? If yes, how<br>
should these isles be corrected?<br>
<br>
Finally, how smooth is the inflated surface expected to be in a &#39;correct&#39;<br>
case? Should a small amount of spikes be allowed, as long as they are not<br>
&#39;too severe&#39;?<br>
<br>
I can upload more images if needed, thanks in advance!<br>
<br>
Kind regards<br>
Nikolas<br>
<br>
</blockquote>
<br>
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