Hi Carolina,
the yellow line represents the gray/white boundary, and so presumably
should follow the bottom of the heterotopia. If it is large though, it
may be difficult to obtain an accurate boundary since it breaks many of
our assumptions (e.g. max thickness, sharp intensity gradient at gray/white
border, ....)
cheers,
Bruce
On Tue, 26 Jul 2011, Carolina
Valencia wrote:
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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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