Try putting some control points near the top. Make sure they are in white matter (and not WM that has been partially volumed). See the tutorial on control points for more details.

doug

Rutvik Desai wrote:

Hello,

We have some signal dropout at the top of the brain in some of our scans. Because of that, the gray/white boundary is not very accurate at the top. The gm tends to be too thick because some of the darkened wm is classified as gm. What particular parameters can we experiment with to correct for this? I am guessing that some things in nu_correct and/or mri_normalize should be adjusted, but what specifically would you recommend? This anatomy is an average of two scans and the FS version is freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5.

thanks, Rutvik

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