From: " andreia " <_andreia_@sapo.pt>
To: "Bruce Fischl" <fischl@nmr.mgh.harvard.edu>
Cc: "Julia Hill" <julia.hill@neura.edu.au>, freesurfer@nmr.mgh.harvard.edu
Sent: Friday, 17 February, 2012 1:01:06 AM
Subject: Re: [Freesurfer] optic nerve inlcuded as pial matter

Since it is such a straightforward correction, I've been making it  
because I thought that it would have some effect (though tiny).

Thanks!
Andreia

Citando Bruce Fischl <fischl@nmr.mgh.harvard.edu>:

> yes, exactly. it will have a tiny effect on total surface area, but  
> that includes noncortical regions anyway
> On Thu, 16 Feb 2012, _andreia_@sapo.pt wrote:
>
>> Ah ok! :)
>>
>> So it won't affect any stats?
>>
>> Anyway, not correcting this will make the inflated surface to have  
>> a prominence, right? In that case it will only look better for  
>> results' displaying.
>>
>> Andreia
>>
>>
>> Citando Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
>>
>>> if they are coincident then it is accurately detected as  
>>> non-cortical and won't affect any thickness/volume corrections, so  
>>> fixing it is really just aesthetic.
>>>
>>> cheer
>>> Bruce
>>>
>>> On Thu, 16 Feb 2012, _andreia_@sapo.pt wrote:
>>>
>>>>
>>>> Hi Julia,
>>>>
>>>> I usually remove the voxels from brainmaks.mgz for the pial edits but also
>>>> from wm.mgz. If you deselect the button of the pial surface in  
>>>> tkmedit, you
>>>> will see that the white matter surface is coincident with the pial, so you
>>>> also need to correct that volume. With wm.mgz as auxiliary volume you can
>>>> erase the voxels from both volumes at the same time, you only  
>>>> need to change
>>>> the brush definitions in Tools -> Configure brush info -> target main and
>>>> aux volume. Don't forget to change back this definition if you  
>>>> want to make
>>>> more corrections to only one volume.
>>>>
>>>> After this I run recon-all -autorecon2-wm -autorecon3.
>>>>
>>>> Cheers,
>>>> Andreia
>>>>
>>>>
>>>>
>>>>
>>>> Citando Julia Hill <julia.hill@neura.edu.au>:
>>>>
>>>>    Good morning,
>>>>
>>>>    I have a question about editing of the pial.  I have noticed
>>>>    that on every single scan (so well over 100), the optic nerve
>>>>    has been included as pial matter (see attached screenshot). 
>>>>    This occurs from between 5 and 10 slices in length.  Will i need
>>>>    to remove the voxels from every scan, and do a recon-all
>>>>    autorecon2-pial? 
>>>>
>>>>    Thank you kindly in advance,
>>>>
>>>>    Julia Hill
>>>>
>>>>    Julia Hill
>>>>    Research Assistant
>>>>
>>>>    School of Psychiatry
>>>>
>>>>    University of New South Wales
>>>>
>>>> [IMAGE]
>>>>
>>>> Previously Prince of Wales Medical Research Institute
>>>>
>>>> www.NeuRA.edu.au
>>>> Barker Street Randwick Sydney NSW 2031 Australia
>>>> PO Box 1165 Randwick Sydney NSW 2031 Australia
>>>> T +61 2 9399 1268 
>>>>
>>>>
>>>>
>>>>
>>>
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>>
>>
>>