Hi,<br><br>I&#39;m a relatively new user of freesurfer, so I don&#39;t have much experience ... but I think I&#39;ve also had problems with recon-all output.<br><br>Posterior part of the brain has been omitted in a number of subjects. <br>
<br>For one of the subjects I have tried to increase the area that is included in the brainmask, but the surfaces were still missing parts of the brain (I don&#39;t have output for the original problem). <br><br>For the same subject, I have then tried to include control points (perhaps too many?), and then I ended up with a really large chunk of the occipital lobe missing.(surfsOnOrig.png &amp; surfsOnBrainmask.png) <br>
<br>surfsOnOrig_2.pmg and surfsOnBrainmask_2.png are from another subject, but you can see an example of how much occipital lobe is missing what happens when I run recon-all. (perhaps it is not too much to do a manual edit?)<br>
<br>I think the problem might be a large difference in the white/gray contrast between occipipal lobe and the rest of the brain. <br><br>Could you please tell me if this is fairly normal amount of brain to be missing and if there is anything that I could do to improve the situation.<br>
<br>Thanks so much in advance.<br><br>Cheers,<br>Branka<br>