Re: [Freesurfer] white matter mask

[Doug Greve]

If you just want white matter, then better to create a mask from the
aparc+aseg.mgz with mri_binarize with the --wm flag.

doug



On Mon, 28 Dec 2009, Bruce Fischl wrote:

> you can use the wm.mgz or filled.mgz volumes for this, or use mris_fill
> to create the interior of the white surface and then take out the aseg
> voxels that are not white
>
> cheers,
> Bruce
>
>
> On Mon, 28 Dec 2009, Oya,
> Hiroyuki wrote:
>
>> Hello All,
>>
>> I'd like to create mask of white matter. Would it be possible to use white 
>> matter surface to do this?
>>
>> Tx.
>>
>> Hhiroyuki
>>
>>
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>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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[Freesurfer] white matter mask

[Oya, Hiroyuki]

Hello All,

I'd like to create mask of white matter. Would it be possible to use white 
matter surface to do this?

Tx.

Hhiroyuki

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Re: [Freesurfer] white matter mask

[Bruce Fischl]

you can use the wm.mgz or filled.mgz volumes for this, or use mris_fill 
to create the interior of the white surface and then take out the aseg 
voxels that are not white

cheers,
Bruce


On Mon, 28 Dec 2009, Oya, 
Hiroyuki wrote:

> Hello All,
>
> I'd like to create mask of white matter. Would it be possible to use white 
> matter surface to do this?
>
> Tx.
>
> Hhiroyuki
>
>
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Re: [Freesurfer] white matter mask

[Douglas N Greve]

yes, or you can use aparc+aseg.mgz. They should give the same result.

Mehul Sampat wrote:
> I just realized that a simpler way to create this mask would be to use 
> "ribbon.mgz" and find all the voxels with the labels 2 and 41 which 
> correspond to "Left_White" and "Right_White".
> https://surfer.nmr.mgh.harvard.edu/fswiki/mris%25volmask
> Does this sound correct ? 
>
> Mehul
>
>
> On Sun, Nov 8, 2009 at 1:48 PM, Mehul Sampat  > wrote:
>
> Hi Folks,
>
> I want to create a white matter mask (a volume in which all of the
> white matter voxels are 1 and 0 otherwise)
>
> For this, I am planning to use wmparc.mgz and then set the voxels
> with labels of wm-lh-? and wm-rh-? as 1.
> (here wm-lh-? represents labels such wm-lh-temporalpole,
> wh-lh-insula etc)
> From wmparc.stats I found there are 35 such labels for each
> hemisphere.
>
> Is this the right way to create the white matter mask ? 
>
> Thanks
> Mehul 
>
>
> 
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] white matter mask

[Mehul Sampat]

I just realized that a simpler way to create this mask would be to use
"ribbon.mgz" and find all the voxels with the labels 2 and 41 which
correspond to "Left_White" and "Right_White".
https://surfer.nmr.mgh.harvard.edu/fswiki/mris%25volmask
Does this sound correct ?

Mehul


On Sun, Nov 8, 2009 at 1:48 PM, Mehul Sampat  wrote:

> Hi Folks,
>
> I want to create a white matter mask (a volume in which all of the white
> matter voxels are 1 and 0 otherwise)
>
> For this, I am planning to use wmparc.mgz and then set the voxels with
> labels of wm-lh-? and wm-rh-? as 1.
> (here wm-lh-? represents labels such wm-lh-temporalpole, wh-lh-insula etc)
> From wmparc.stats I found there are 35 such labels for each hemisphere.
>
> Is this the right way to create the white matter mask ?
>
> Thanks
> Mehul
>
>
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[Freesurfer] white matter mask

[Mehul Sampat]

Hi Folks,

I want to create a white matter mask (a volume in which all of the white
matter voxels are 1 and 0 otherwise)

For this, I am planning to use wmparc.mgz and then set the voxels with
labels of wm-lh-? and wm-rh-? as 1.
(here wm-lh-? represents labels such wm-lh-temporalpole, wh-lh-insula etc)
>From wmparc.stats I found there are 35 such labels for each hemisphere.

Is this the right way to create the white matter mask ?

Thanks
Mehul
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