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Thanks for getting back to me. I've recently asked for help in another
thread and sent in the subject directory because the control points didn't
work well after my attempt. But I'll take your advice and give it
another try.
Thank you!
On Fri, Jan 31,
It is hard to say from that image because of the aseg, but it looks like
the white surface is not extending far enough and so the pial surface
starts too far away to get all the way out. You might need some control
points in the WM in that area
On 1/28/2020 7:56 PM, Monica Bondy wrote:
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Sorry for the very late reply and not explaining the problem well in the
first place. I would still appreciate your assistance if possible.
Like some other threads that are on the archive, I was experiencing the
problem where the pial surface wasn't get
Hi Monica
hmmm, hard to say without seeing the dataset. You could try using expert
options to change some of the intensity thresholds if this is something
specific to your acquiisition. If you upload the gzipped subject dir we
will take a look
cheers
Bruce
On Fri, 13 Dec 2019, Monica Bondy
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 gra
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 measure
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
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 o
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.
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 kn
Hi Carolina,
To correct the red surface (pial surface), you can follow this tutorial
here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits
If some WM is labeled as GM, then most likely you'll need to do some white
matter edits by adding more wm voxels to the wm.mgz to extend the
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 surf
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