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 <[email protected]> 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 <[email protected]>
>> 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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>>
>> <wrong_surfs_c39.jpg>
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Sebastian Moeller
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