Hi Doug,

thank for your suggestion.  I will give it a try.

Yang

On Tue, Jan 11, 2011 at 10:57 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
You can also run defect-seg to create segementations and annotations of the defects. This can be quite handy when tracking down defects. Run it with --help to get info on how to use it.

doug


Bruce Fischl wrote:
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.edu>wrote:

   
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.de><sebastian.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 no
aseg 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.com><liu.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.edu><khoa@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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