Hi Vadim,
sometimes there is a single edge left when you make the cut that connects across it. Can you zoom in and check? Usually this is easiest if you overlay the wireframe. You can also try "dilate cuts" and flatten to see if that removes the problem, although you will lose another mm of cortex that way.
cheers Bruce
On Sun, 4 Apr 2010, Vadim Axel wrote:
Dear all,
For one of my brains I fail to flatten correctly occipital lobe neither for rh, nor for lh (I get 'closed' patch). I tried to make several cut planes with different calcarine cut lines, but the result was the same. I attach a screenshot of rh with three of my attempts and the reconstructed full brain (resized it a little to fit the screenshot).I run: mris_flatten -w 0 -distances 20 20 command. Any idea what exactly might have gone wrong? How crucial is to have the calcarine cut and cut plane to be exactly on its place in order to achieve successful flattening procedure?
I am using Ubuntu VirtualBox FreeSurfer v4.5 version.
Thanks a lot, Vadim