Hi Bruce,

Yes, it should be classified as a gray matter, if I save a point of an heterotopia in the tkmedit and then open it in tksurfer the point showed at the inflated surface correspond to that point or to the projection of the heterotopia in the cortical surface?
what happen with these measures if sometimes the heterotopias are outlined by the yellow line and sometimes are not?
I don't know if I'm totally clear.

Thanks,

Best,

Carolina


2011/7/21 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Hi Carolina,

no, the aseg cortex/wm is not used for thickness or volume (it can be, but we don't recommend it). The surfaces are.  As for the heterotopias, I don't really know what a good output would be. It depends what you want to do with them. I guess they should be gray matter, no?

Bruce



On Thu, 21 Jul 2011, Carolina Valencia wrote:

Hi Bruce,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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