Hi Matt,

this is almost certainly a topology correction problem, not a control point one. You can see from your snapshots how the superior temporal gyrus is (incorrectly) disconnected from the body of the temporal lobe. This results in a topological defect, that is incorrectly fixed by the topology correction algorithm to remove the whole white matter strand. Try adding some voxels to the wm.mgz to reconnect it and make sure that it stays connected. Note that it's impossible to judge whether it is a defect from a single slice. You need to look at multiple slices/views to be sure. In this case you would move forward and backwards coronally. Once the strand disconnects, it has to stay disconnected as you move in the same direction, otherwise it is a handle. In this case you would want to fill in the hole/handle to make sure that it stays connected.

cheers, Bruce

On Fri, 21 Dec 2007, Matt Colvin wrote:

Freesurfer Folks,

I am having trouble with a handful of subjects in which there are portions of white and grey matter not included by the white and pial surfaces. The problems at hand seemed like good candidates for control points, so I added some and have run recon2-cp on these subjects (in FreeSurfer v 4.0.1). I am having limited success fixing the problems, especially in the temporal lobes, and have attached a couple screen caps of one of the more egregious problems. Most of the voxels I believe to be white matter are in the 100-110 range of intensity. If it can be guessed at from these screen shots, is there some principle of using control points that I am not getting right? Also, would editing the wm.mgz file be another possible avenue of fixing the problem? As always, thanks in advance.

--Matt Colvin