Hi, I finished reconstructing a monkey's surface following the scripts on the wiki. The output surfaces seems to be a bit distorted and rough around the edges. This reconstruction is done with a volume normalized by using ~400 white matter control points. The resolution of the scan is 1x1x1 mm. Here are some pictures to look at: http://www.flickr.com/photos/52445793@N05/sets/72157624471174691/
Interestingly, white matter and gray matter boundaries seem to be intermingled for some reason. I was hoping control points would take care of that problem but they didn't. This can be observed by the 2 vol_surf images in the set.
The most obvious defects can be seen on the white matter. There are small protrusions over the gyri, and the surfaces are generally very rough, unlike a successful human reconstruction.
I was wondering if you have any ideas as to the source of the problem. Skull stripping was done with FSL's bet, and it looks successful. Can it be a problem with intensity normalization?
Regards, Ali Arslan