Hi Chuck, The certain area in your snapshots you are refering to is the medial temporal lobe (hemisphere on left side of the image)? In the snapshots you have the pial, wm, and orig surface displayed. Please verify that the yellow line corresponds to the wm surface and not the orig surface. What type of edits did you make the second time around which had no effect? -Louis

On Tue, 10 Jul 2012, Charles Frank wrote:

Freesurfer experts,

I am having problems generating a corrected wm boundary after editing the wm.mgz volume. After control points were placed and ran with the command autorecon2-cp, I noticed that the yellow line became overzealous and included gm in some of the slices. To fix this I followed the tutorial “fixing Non-white matter classified as white matter”. I fixed all the slices that had the problem in a certain area. However, after running autorecon2-wm and autorecon3 the edits to the wm.mgz volume remain and yellow line does not change....i.e. The edits that were made remained, but had absolutely no effect on the wm boundary. I am using version 5.0.

I have included some screen shots of a certain area that was targeted correction. These shots are taken after the data was ran through autorecon2-wm and autorecon3.

Any suggestions of what I'm doing wrong would be very appreciated.

Thanks Chuck