Hi Alia,

that's a tough one as it will be difficult to recover the true geometry/topology. What do you think it should do in this case? The images you sent seemed like reasonable representations of the anatomy to me. I guess you could try filling in the hole in the wm.mgz. Definitely do *not* put control points in the lesion. That will mess everything up.

cheers, Bruce

On Wed, 9 Sep 2009, Lemkaddem Alia wrote:

Hi,

One of our subjects has a big lesion in the left hemisphere, which appears on the MRI. Because of this, I obtain a big whole in the cortical parcellation.

I have already tried:

• To correct the WM mask.
• Used control points to fix intensity normalization.

Please have a look at the images that I have attached. The lesion is very big and it's very hard to tell where the WM is.

Thankful for all the help I can get,

Alia