Hi Yang,
if you send us the surfaces and the wm.mgz/brainmask.mgz we'll take a look. You need to find the reason for the topological defect in the wm.mgz. By defition to correct a defect the orig (green) surface can no longer follow the boundary of the wm.mgz. If it did it would have a defect! You can also look at the orig.nofix and/or the inflated.nofix to see where the defect is in that region
cheers Bruce
On Tue, 11 Jan 2011, Yang Liu wrote:
Hi Bruce,
I followed the tutorial at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits.
But I couldn't find similar examples as mine in the tutorial. I don't really understand why don't the yellow and green surfaces follow the boundary of wm.mgz, especially the boundary is well defined in the slices.
Yang
On Mon, Jan 10, 2011 at 10:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Not without scrolling through the wm volume. You will need to edit it. Have you done the troubleshooting tutorial?
On Jan 10, 2011, at 10:48 PM, Yang Liu liu.yang76@gmail.com wrote:
Hi Bruce,
Do you know how to fix it?
Yang
On Mon, Jan 10, 2011 at 10:43 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu fischl@nmr.mgh.harvard.edu> wrote:
Then I must be a topologica defect
On Jan 10, 2011, at 10:37 PM, Yang Liu < liu.yang76@gmail.com liu.yang76@gmail.com> wrote:
Hi Sebastian,
Yes. It is Macaque. There is no aseg.
Yang
On Mon, Jan 10, 2011 at 10:15 PM, Sebastian Moeller <sebastian.moeller1@rwth-aachen.desebastian.moeller1@rwth-aachen.de sebastian.moeller1@rwth-aachen.de> wrote:
Hi All,
On Jan 10, 2011, at 19:12 , Bruce Fischl wrote:
Does the aseg label that as ventricle?
This pretty much looks like macaque data, so I think there is noaseg for that. I would love to be corrected on that point though.
Best Sebastian
On Jan 10, 2011, at 9:34 PM, Yang Liu < liu.yang76@gmail.comliu.yang76@gmail.com
liu.yang76@gmail.com> wrote:
Hi Khoa,
Thanks for your reply. I attached the snapshot of the same slice with brainmask.mgz. You can
see clearly that the green and yellow surface at the wrong regions. They doesn't look like ventricles to me.
It is strange that even the green surface doesn't follow the original
wm.mgz, though the wm.mgz as attached in the previous email
has very well defined boundaries near the wrong regions. Any idea to correct this?
Yang
On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen <khoa@nmr.mgh.harvard.edukhoa@nmr.mgh.harvard.edu
khoa@nmr.mgh.harvard.edu> wrote:
Hi Yang,
To edit the pial surface, you want to use brainmask.mgz.
As for the wm.mgz, you're right in that control points isn't the
solution. Control points are to fix intensity problem, but you can also add wm voxels manually to fix any wm defects. In this case, adding that many control points would probably make the situation worse because the entire area will brighten and that would potentially extend the surfaces to include grey matter.
Is the area you pointed out by any chance the ventricle? If it is,
then it doesn't matter that the white surface includes it. It's hard to tell with just this image. Do you mind sending a snapshot of the brainmask.mgz for this slice?
On Mon, 10 Jan 2011, Yang Liu wrote:
Hi Freesurferers,
I am correcting some defects in the white matter surface (yellow) and
the
pial surfaces (red). But I am not very sure of which volume I should
work
on. I did several experiments on editing one volume at a time.
For pial (the red) surface, I edited brain.mgz first. I found it
corrected
some pial defects. However, I found one previous post here said the volume that should be edited is brainmask.mgz. So the second time I only changed brainmask.mgz. It also works.
So, which one should I work on?
brian.mgz or brainmask.mgz?
Also, for defects on the white matter surface (the yellow one), I
found the
surface doesn't follow the white matter segmentation closely, although
I
have a good wm.mgz. (see attached image). At the location pointed by the red arrow in the attached image, both
the
green and yellow sufaces includes a lot of gray matter at the
location. It
is strange that the wm.mgz has a very well defined slice in that neighborhood. I am familiar with situations where the surfaces miss a few white
matter
pixels, for which I can add a few control points to improve it.
How shall I edit wm.mgz to correct this? Adding more control points
is not
a solution, apparently.
Thank you.
Yang
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