@ Louis, no I didn't correct the WM mask yet. But since it's a step clearly 'behind' correcting the skull strip and adding control points, and it takes a lot of work to accurately draw the WM mask, I would prefer to automate things as much as possible...

@Alan, thanks for your suggestion - although 1 CP for 2 voxels appears to be a lot. Tomorrow I'll check whether adding CP's helps.

On Mon, Mar 12, 2012 at 3:47 PM, Alan Francis <alandarkenergy@gmail.com> wrote:

Hi Martijn:

In our lab, we basically add a greater density of control points - almost 1 CP for every 2 voxels. This way the corrected pial looks closer to what's expected.

best,

Alan

BIDMC

On Mon, Mar 12, 2012 at 5:38 AM, Martijn Steenwijk <martijnsteenwijk@gmail.com> wrote:

Dear all,

I've been correcting a recon with controlpoints and correction of the skull strip. Although the result is a lot better, still a part of the temporal lobe is missed, although I have been putting control points in this area. Is there a way to improve this? See attached image (left: pre-correction, right: post-correction).

Best,
Martijn

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