thanks for your explanation. I was thinking the the segmentation region is used to calculate cortical thickness, by the way, is it used for calculate something? such as the GM volumes? I want to know this to be sure if in some point I have to fix this.

About the heterotopias, is a good output to have someones classified as WM, other as GM and sometimes are outlined by the yellow line and sometimes are not?

Best regards,

Carolina

2011/7/19 Bruce Fischl <fischl@nmr.mgh.harvard.edu>

Hi Carolina,

it looks mostly to me like the surfaces are in the right place (the yellow and red lines). Don't look at the colored overlay - that is the aseg voxel segmentation and not what we typically use for cortical morphometry. Only look at the yellow and red lines.

cheers
Bruce
On Tue, 19 Jul 2011, Carolina Valencia wrote:

tiff I guess, I took the pictures from FS

2011/7/19 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
what format are the files in the archive in? They don't have an extension

On Tue, 19 Jul 2011, Carolina Valencia wrote:

I hope this attachement works.I also noticed that some heterotopias are classified as WM, other as GM and sometimes are outlined by the yellow line and
sometimes are not.

Best regards,

Carolina

2011/7/19 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
   Hi Carolina,

   can you gzip it or use compression? Usually people can send a few images to the list.

   cheers
   Bruce
   On Tue, 19 Jul 2011, Carolina Valencia wrote:

   Dear FS experts,
   I'm trying to analyse a case of cortical dysplasia, but after recon-all I see some errors in tkmedit that I don't know what to edit. I found some
errors
   in cortical and
   subcortical segmentation, I don't find in the failure mode presentation a way to solve this.
   I saw the pial surface (yellow line) with acceptable accuracy but the GM (the red one) in some regions are misplaced (WM classified as GM and some
GM not
   classified (empty
   color))
   I tried to attached an image to illustrate the problem but I don't succeed, because the mailing list reject my email. How I can send you an image of
   ~700kb?

   Thanks a lot,

   Carolina

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