Hi Khoa,

Thanks for your reply.
I attached the snapshot of the same slice with brainmask.mgz. You can see clearly that the green and yellow surface at the wrong regions. They doesn't look like  ventricles to me. 
It is strange that even the green surface doesn't follow the original wm.mgz, though the wm.mgz as attached in the previous email
has very well defined boundaries near the wrong regions.
Any idea to correct this?


Yang


On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen <khoa@nmr.mgh.harvard.edu> wrote:
Hi Yang,

To edit the pial surface, you want to use brainmask.mgz.

As for the wm.mgz, you're right in that control points isn't the solution. Control points are to fix intensity problem, but you can also add wm voxels manually to fix any wm defects. In this case, adding that many control points would probably make the situation worse because the entire area will brighten and that would potentially extend the surfaces to include grey matter.

Is the area you pointed out by any chance the ventricle? If it is, then it doesn't matter that the white surface includes it. It's hard to tell with just this image. Do you mind sending a snapshot of the brainmask.mgz for this slice?


On Mon, 10 Jan 2011, Yang Liu wrote:

Hi Freesurferers,

I am correcting some defects in the white matter surface (yellow) and the
pial surfaces (red). But I am not very sure of which volume I should work
on.
I did several experiments on editing one volume at a time.

For pial (the red) surface, I edited brain.mgz first. I found it corrected
some pial defects.
However, I found one previous post here said the volume that should be
edited is brainmask.mgz.
So the second time I only changed brainmask.mgz. It also works.

So, which one should I work on?

brian.mgz or brainmask.mgz?

Also, for defects on the white matter surface (the yellow one),  I found the
surface doesn't follow the white matter segmentation closely, although I
have a good wm.mgz. (see attached image).
At the location pointed by the red arrow in the attached image, both the
green and yellow sufaces includes a lot of gray matter at the location. It
is strange that the wm.mgz has a very well defined slice in that
neighborhood.
I am familiar with situations where the surfaces miss a few white matter
pixels, for which I can add a few control points to improve it.

How shall I edit wm.mgz to correct this?  Adding more control points is not
a solution, apparently.

Thank you.

Yang



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