Hi Branka

those are really big bias fields in your data that are causing the problems. Can you tell us about the acquisitions? What field strength? Scanner? Coil? Sequence?

thanks Bruce

On Mon, 1 Aug 2011, Branka Milivojevic wrote:

Hi,

I'm a relatively new user of freesurfer, so I don't have much experience ... but I think I've also had problems with recon-all output.

Posterior part of the brain has been omitted in a number of subjects.

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't have output for the original problem).

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 & surfsOnBrainmask.png)

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?)

I think the problem might be a large difference in the white/gray contrast between occipipal lobe and the rest of the brain.

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.

Thanks so much in advance.

Cheers, Branka