Hi Bruce,
Thank you for your response!
Actually, after reviewing multiple papers ( segmentation in
Freesurfer) I
found that using "wmparc.mgz" as an input in the command "mri_binarize"
will enable me to create two mask ( depending on the white matter
parcellate
mentioned in wmparc.mgz): The first mask is for deep white matter and
the
second mask is for the outer white matter.
I am facing one problem right now. I don't know how to divide the white
matter parcellates mentioned in "wmparc.mgz" into deep and outer
parcellates. Is there any reference that can help. The number of the
parcellate is very big and for the purposes of publication I need a
reference to divide them.
Any help is highly appreciated.
Bests,
John Anderson
Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
Sent: Saturday, September 05, 2015 at 4:23 PM
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Segmenting deep and outer white matter
Hi John
sorry, meant to respond but spaced it. Have you checked out the
wmparc.mgz? It may have what you need.
cheers
Bruce
On Sat, 5 Sep 2015, John Anderson
wrote:
> Hi Freesurfers,
> I am interested in studying the difference between the outer and deep
white
> matter volume in my study groups.
>
> I am thinking in the following procedures:
> 1. If there is any way in Freesurfer to do segmentation for the white
matter
> (only in the depth of 3 cm) starting from the cortex. Then second
> segmentation for the deep white matter. Is this possible in
Freesurfer?
> 2. Creating a mask ( using mri_binarize) for all the superficial white
> matter Freesurfer's labels and another mask for the deep white
matter (
how
> can I find the Freesurfer deep white matter labels and the outer
white
> matter labels ?)
> 3. If there is any atlas that can separate the outer and deep white
matter
> then running recon-all depending on this new atlas.
>
> Thanks in advance for any suggestion.
> John
>
>
> Bests,
> John Anderson
>
> Senior Research Associate
> Psychological and Brain Sciences Dept.
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834
> Fax: +1 (603) 646-1419
>
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